Varios Post Type con la misma taxonomia

Gracias por tu respuesta Jose.
He probado con get_post_type() pero siempre me devuelve noticia, aunque esté visualizando un term con url de proyectos. El problema está que al tener dos post type la taxonomía, no sabe a cual tiene que pertenecer y no utiliza la url para saberlo.
En el single de proyecto y noticia, me reconoce el post type sin problemas.

Saludos

Buenas Oldlastman, gracias por tu respuesta.

Aquí te pongo el código, pero utilizo los rewrites como podrás ver a continuación:

Creación de post type y la taxonomía, ademas de varias funciones como vista de columnas, filtro de categorías, …:

<?php
	if ( !class_exists( 'PostType' ) ) {

        class PostType {

            function __construct() {
                // Adds the proyecto post type and taxonomies
                	add_action( 'init', array( &$this, 'PostType_init' ), 0 );

                // Adds columns in the admin view for thumbnail and taxonomies
                	$postTypes = array( 'proyecto', 'noticia' );
                	foreach ( $postTypes as $postType ) {
                		add_filter( 'manage_edit-' . $postType . '_columns', array( &$this, 'PostType_edit_columns' ) );                	
                	}
                	add_action( 'manage_posts_custom_column', array( &$this, 'PostType_column_display' ), 10, 2 );

                // Allows filtering of posts by taxonomy in the admin view
                	add_action( 'restrict_manage_posts', array( &$this, 'add_taxonomy_filters' ) );
            }

            function PostType_init() {
            	$postTypes = array( 'proyecto', 'noticia' );

            	foreach ( $postTypes as $postType ) {
        			switch ($postType) {
        				case 'proyecto':
        					$icono = 'dashicons-screenoptions';
        					break;
        				
        				case 'noticia':
        					$icono = 'dashicons-info';
        					break;
        			}

        			// Register Post Types
		                $labels = array(
		                    'name'               => __( $postType . 's' ),
		                    'singular_name'      => __( $postType ),
		                    'add_new'            => __( 'Añadir nuevo' ),
		                    'add_new_item'       => __( 'Añadir nuevo ' . $postType ),
		                    'edit_item'          => __( 'Editar ' . $postType ),
		                    'new_item'           => __( 'Nuevo ' . $postType ),
		                    'view_item'          => __( 'Ver ' . $postType ),
		                    'search_items'       => __( 'Buscar ' . $postType ),
		                    'not_found'          => __( 'No se encontraron ' . $postType . 's' ),
		                    'not_found_in_trash' => __( 'No se encontraron ' . $postType . 's en la papelera' )
		                );

		                $args = array(
		                    'labels'             => $labels,
		                    'public'             => true,
		                    'publicly_queryable' => true,
		                    'show_ui'            => true,
		                    'show_in_menu'       => true,
		                    'show_in_nav_menus'  => true,
		                    'menu_position '     => 20,
		                    'supports'           => array( 'title', 'editor', 'thumbnail', 'page-attributes', 'post-formats', 'revisions' ),
		                    'capability_type'    => $postType,
		                    'capabilities'       => array(
		                        'edit_post'           => 'edit_' . $postType,
		                        'read_post'           => 'read_' . $postType,
		                        'delete_post'         => 'delete_' . $postType,
		                        'edit_posts'          => 'edit_' . $postType . 's',
		                        'edit_others_posts'   => 'edit_others_' . $postType . 's',
		                        'publish_posts'       => 'publish_' . $postType . 's',
		                        'read_private_posts'  => 'read_private_' . $postType . 's',
		                        'create_posts'        => 'edit_' . $postType . 's',
		                        'delete_posts'        => 'delete_' . $postType . 's',
		                        'delete_others_posts' => 'delete_others_' . $postType . 's',
		                    ),
		                    'hierarchical'       => false,
		                    'has_archive'        => $postType,
		                    'rewrite'            => array(
		                        'slug'           => $postType . '-item',
		                        'hierarchical'   => true,
		                        'with_front'     => false
		                    ),
		                    'menu_icon'          => $icono
		                );

		                $args = apply_filters( $postType . '_args', $args );		                
		                register_post_type( $postType, $args );
                }

                // Registrar las taxonomias
	                $taxonomy_departamento_labels = array(
	                    'name'                       => __( 'Departamentos'),
	                    'singular_name'              => __( 'Departamento'),
	                    'search_items'               => __( 'Buscar Departamentos'),
	                    'popular_items'              => __( 'Departamentos Populares'),
	                    'all_items'                  => __( 'Todas los Departamentos'),
	                    'parent_item'                => __( 'Padre del Departamento'),
	                    'parent_item_colon'          => __( 'Padre del Departamento:'),
	                    'edit_item'                  => __( 'Editar el Departamento' ),
	                    'update_item'                => __( 'Actualizar el Departamento' ),
	                    'add_new_item'               => __( 'Añadir nuevo Departamento' ),
	                    'new_item_name'              => __( 'Nuevo Departamento' ),
	                    'separate_items_with_commas' => __( 'Separar los Departamentos por comas' ),
	                    'add_or_remove_items'        => __( 'Añadir o Borrar Departamentos' ),
	                    'choose_from_most_used'      => __( 'Elegir entre los Departamentos mas usados' ),
	                    'menu_name'                  => __( 'Departamentos' ),
	                );

	                $taxonomy_departamento_args = array(
	                    'labels'            => $taxonomy_departamento_labels,
	                    'public'            => true,
	                    'capabilities'      => array(
	                        'manage_terms'  => 'manage_departamentos',
	                        'edit_terms'    => 'edit_departamentos',
	                        'delete_terms'  => 'delete_departamentos',
	                        'assign_terms'  => 'assign_departamentos',
	                    ),
	                    'hierarchical'      => true,
	                    'show_ui'           => true,
	                    'rewrite'           => array(
	                        'slug'          => 'departamento',
	                        'hierarchical'  => true,
	                        'with_front'    => false
	                    ),
	                    'meta_box_cb'       => 'departamento_select_meta_box',
	                );

	                $taxonomy_departamento_args = apply_filters( 'taxonomy_departamento_args', $taxonomy_departamento_args);	                
	                register_taxonomy( 'departamento', $postTypes, $taxonomy_departamento_args );

	            // Select MetaBox
	                function departamento_select_meta_box( $post, $box ) {
	                    $defaults = array( 'taxonomy' => 'departamento' );

	                    if ( ! isset( $box['args'] ) || ! is_array( $box['args'] ) ) {
	                        $args = array();
	                    } else {
	                        $args = $box['args'];
	                    }

	                    $r        = wp_parse_args( $args, $defaults );
	                    $tax_name = esc_attr( $r['taxonomy'] );
	                    $taxonomy = get_taxonomy( $r['taxonomy'] );
?>
	                    <div id="taxonomy-<?php echo $tax_name; ?>" class="categorydiv">
	                        <div id="<?php echo $tax_name; ?>-all" class="tabs-panel">
<?php
	                            $name = ( $tax_name == 'departamento' ) ? 'post_category' : 'tax_input[' . $tax_name . ']';
	                            echo "<input type='hidden' name='{$name}[]' value='0' />"; // Allows for an empty term set to be sent. 0 is an invalid Term ID and will be ignored by empty() checks.
?>
	                            <ul id="<?php echo $tax_name; ?>checklist" data-wp-lists="list:<?php echo $tax_name; ?>" class="categorychecklist form-no-clear">
	                                <?php wp_terms_checklist( $post->ID, array( 'taxonomy' => $tax_name, 'checked_ontop' => false, 'walker' => new Walker_Checklist(), ) ); ?>
	                            </ul>
	                        </div>
	                    </div>
<?php
                	}
            }

            // Columns Post Type
	            function PostType_edit_columns( $columns ) {
	                $columns['thumbnail'] 	 = __( 'Thumbnail' );
	                $columns['departamento'] = __( 'Departamento' );
	                $columns['galeria']   	 = __( 'Galeria' );
	                $columns['visitas']   	 = __( 'Visitas' );
	                return $columns;
	            }

	            function PostType_column_display( $PostType_columns, $post_id ) {
	                switch ( $PostType_columns ) {
	                    case 'thumbnail':
	                        $width          = (int) 80;
	                        $height         = (int) 80;
	                        $thumbnail_id   = get_post_meta( $post_id, '_thumbnail_id', true );

	                        // Display the featured image in the column view if possible
	                        if ( $thumbnail_id ) {
	                            $thumb = wp_get_attachment_image( $thumbnail_id, array( $width, $height ), true );
	                        }
	                        if ( isset( $thumb ) ) {
	                            echo $thumb;
	                        } else {
	                            echo __( 'None' );
	                        }
	                    	break;

	                    case 'departamento':
	                        if ( $category_list     = get_the_term_list( $post_id, 'departamento', '', ', ', '' ) ) {
	                            if ( is_admin() ) {
	                                $terms          = get_the_terms( $post_id, 'departamento' );
	                                foreach ( $terms as $term) {
	                                    $term_padre = $term->parent;
	                                }
	                                $term_father    = get_term_by( 'id', $term_padre, 'departamento' );
	                                echo $term_father->name . ' - ' . $category_list;
	                            } else {
	                                echo $category_list;
	                            }
	                        } else {
	                            echo __( 'None' );
	                        }
	                    	break;

	                    case 'galeria':

	                        $post_id = get_the_id();
	                        if ( $post_id ) {
	                            echo $post_id;
	                        } else {
	                            echo __( 'None' );
	                        }
	                    	break;

	                    case 'visitas':
	                        $post_id    = get_the_id();
	                        $count_key  = 'post_views_count';
	                        $count      = get_post_meta( $post_id, $count_key, true );
	                        echo $count;
	                    	break;
	                }
	            }

            // Filtro Departamentos
	            function add_taxonomy_filters() {
	                global $typenow, $current_user;
	                get_currentuserinfo();

	                // An array of all the taxonomyies you want to display. Use the taxonomy name or slug
	                $taxonomies = array( 'departamento' );

	                // must set this to the post type you want the filter(s) displayed on
	                if ( $typenow == 'proyecto' || $typenow == 'noticia' ) {
	                    $permisos = of_get_option( $current_user->id . 'permisos' );

	                    foreach ( $taxonomies as $tax_slug ) {
	                        $current_tax_slug   = isset( $_GET[$tax_slug] ) ? $_GET[$tax_slug] : false;
	                        $tax_obj            = get_taxonomy( $tax_slug );
	                        $tax_name           = $tax_obj->labels->name;
	                        $terms              = get_terms( 'departamento', array( 'post_type' => $typenow, 'fields' => 'all' ) );

	                        if ( count( $terms ) > 0 ) {
	                            echo "<select name='$tax_slug' id='$tax_slug' class='postform'>";
	                            echo "<option value=''>$tax_name</option>";

	                            foreach ( $terms as $term ) {
	                                if ( $permisos[$term->term_id] == '1' || $current_user->roles[0] == 'administrator' ) {
	                                    echo '<option style="font-weight: bold;" value=' . $term->slug, $current_tax_slug == $term->slug ? ' selected="selected"' : '','>' . $term->name . ' ( ' . $term->count .')</option>';
	                                    $parent = $term->term_id;
	                                } else {
	                                    $term_parent = get_term_top_most_parent( $term->term_id, 'departamento' );
	                                    if ( $parent == $term_parent['parent'] ) {
	                                            switch ( $term_parent['contador'] ) {
	                                                case '1':
	                                                    $estilo = 'color: red';
	                                                    break;

	                                                case '2':
	                                                    $estilo = 'color: green';
	                                                    break;
	                                            }

	                                        echo '<option style="' . $estilo . '" value=' . $term->slug, $current_tax_slug == $term->slug ? ' selected="selected"' : '','>' . $term->name . ' ( ' . $term->count .')</option>';
	                                    }
	                                }
	                            }
	                            echo "</select>";
	                        }
	                    }
	                }
	            }
        }
    }
    new PostType;

Todo lo relacionado con rewrite rules:

// Rewrites rules Noticias
       	add_action( 'generate_rewrite_rules', 'register_PostType_rewrite_rules' );
        function register_PostType_rewrite_rules( $wp_rewrite ) {
            $new_rules = array( 
                PostType_lang_rewrite('proyecto') . '/([^/]+)/?$' => 'index.php?departamento=' . $wp_rewrite->preg_index( 1 ),
                PostType_lang_rewrite('proyecto') . '/([^/]+)/([^/]+)/?$' => 'index.php?post_type=proyecto&departamento=' . $wp_rewrite->preg_index( 1 ) . '&proyecto=' . $wp_rewrite->preg_index( 2 ),
                PostType_lang_rewrite('proyecto') . '/([^/]+)/([^/]+)/page/(\d{1,})/?$' => 'index.php?post_type=proyecto&departamento=' . $wp_rewrite->preg_index( 1 ) . '&paged=' . $wp_rewrite->preg_index( 3 ),
                PostType_lang_rewrite('proyecto') . '/([^/]+)/([^/]+)/([^/]+)/?$' => 'index.php?post_type=proyecto&departamento=' . $wp_rewrite->preg_index( 2 ) . '&proyecto=' . $wp_rewrite->preg_index( 3 ),
                PostType_lang_rewrite('proyecto') . '/([^/]+)/([^/]+)/([^/]+)/([^/]+)/?$' => 'index.php?post_type=proyecto&departamento=' . $wp_rewrite->preg_index( 3 ) . '&proyecto=' . $wp_rewrite->preg_index( 4 ),

                PostType_lang_rewrite('noticia') . '/([^/]+)/?$' => 'index.php?departamento=' . $wp_rewrite->preg_index( 1 ),
                PostType_lang_rewrite('noticia') . '/([^/]+)/([^/]+)/?$' => 'index.php?post_type=noticia&departamento=' . $wp_rewrite->preg_index( 1 ) . '&noticia=' . $wp_rewrite->preg_index( 2 ),
                PostType_lang_rewrite('noticia') . '/([^/]+)/([^/]+)/page/(\d{1,})/?$' => 'index.php?post_type=noticia&departamento=' . $wp_rewrite->preg_index( 1 ) . '&paged=' . $wp_rewrite->preg_index( 3 ),
                PostType_lang_rewrite('noticia') . '/([^/]+)/([^/]+)/([^/]+)/?$' => 'index.php?post_type=noticia&departamento=' . $wp_rewrite->preg_index( 2 ) . '&noticia=' . $wp_rewrite->preg_index( 3 ),
                PostType_lang_rewrite('noticia') . '/([^/]+)/([^/]+)/([^/]+)/([^/]+)/?$' => 'index.php?post_type=noticia&departamento=' . $wp_rewrite->preg_index( 3 ) . '&noticia=' . $wp_rewrite->preg_index( 4 ),
            );

            $wp_rewrite->rules = $new_rules + $wp_rewrite->rules;
        }

        // A hacky way of adding support for flexible custom permalinks
        // There is one case in which the rewrite rules from register_kb_rewrite_rules() fail:
        // When you visit the archive page for a child section(for example: http://example.com/noticia/category/child-category)
        // The deal is that in this situation, the URL is parsed as a Knowledgebase post with slug "child-category" from the "category" section
        function fix_PostType_subcategory_query($query) {
        	$postTypes = array( 'proyecto', 'noticia' );

        	foreach ( $postTypes as $postType ) {
	            if ( isset( $query['post_type'] ) && $postType == $query['post_type'] ) {
	                if ( isset( $query[$postType] ) && $query[$postType] && isset( $query['departamento'] ) && $query['departamento'] ) {
	                    $query_old = $query;
	                    // Check if this is a paginated result(like search results)
	                    if ( 'page' == $query['departamento'] ) {
	                        $query['paged'] = $query['name'];
	                        unset( $query['departamento'], $query['name'], $query[$postType] );
	                    }
	                    // Make it easier on the DB
	                    //$query['fields'] = 'ids';
	                    $query['posts_per_page'] = 1;

	                    // See if we have results or not
	                    $_query = new WP_Query( $query );
	                    if ( ! $_query->posts ) {
	                        $query = array( 'departamento' => $query[$postType] );
	                        if ( isset( $query_old['departamento'] ) && 'page' == $query_old['departamento'] ) {
	                            $query['paged'] = $query_old['name'];
	                        }
	                    }
	                }
	            }
	        }

            return $query;
        }
        add_filter( 'request', 'fix_PostType_subcategory_query', 10 );

        function PostType_article_permalink( $article_id, $section_id = false, $leavename = false, $only_permalink = false ) {
            $taxonomy   = 'departamento';
            $article    = get_post( $article_id );

            $return     = '<a href="';
            $permalink  = ( $section_id ) ? trailingslashit( get_term_link( intval( $section_id ), 'departamento' ) ) : home_url( '/' . PostType_lang_rewrite(get_post_type()) . '/' );
            $permalink .= trailingslashit( ( $leavename ? "%$article->post_type%" : $article->post_name ) );
            $return    .= $permalink . '/" >' . get_the_title( $article->ID ) . '</a>';
            return ( $only_permalink ) ? $permalink : $return;
        }

        function filter_PostType_post_link( $permalink, $post, $leavename ) {
            if ( get_post_type( $post->ID ) == 'proyecto' || get_post_type( $post->ID ) == 'noticia' ) {
                $terms      = wp_get_post_terms( $post->ID, 'departamento' );
                $term       = ( $terms ) ? $terms[0]->term_id : false;
                $permalink  = PostType_article_permalink( $post->ID, $term, $leavename, true );
            }
            return $permalink;
        }
        add_filter( 'post_type_link', 'filter_PostType_post_link', 100, 3 );

        function filter_PostType_section_terms_link( $termlink, $term, $taxonomy = false ) {
            if ( $taxonomy == 'departamento' ) {
                $section_ancestors = get_ancestors( $term->term_id, $taxonomy );
                krsort( $section_ancestors );
                $termlink =  home_url( '/' . PostType_lang_rewrite(get_post_type()) . '/' );
                foreach ( $section_ancestors as $ancestor ) {
                    $section_ancestor = get_term( $ancestor, $taxonomy );
                    $termlink .= $section_ancestor->slug . '/';
                }
                $termlink .= trailingslashit( $term->slug );
            }

            return $termlink;
        }
        add_filter( 'term_link', 'filter_PostType_section_terms_link', 100, 3 );

    // Traducir la url en castellano o ingles, noticia o new
        function PostType_lang_rewrite($posttype) {
            // IDIOMA
                $blog   = MslsBlogCollection::instance()->get_current_blog();
                $idioma = $blog->get_description();

            // VARIABLES
                if ( $idioma == 'ES' ) {
                	if ( $posttype == 'proyecto' ) {
                		$clave = 'proyecto';
                	} else {
                		$clave = 'noticia';
                	}
                } else {
                	if ( $posttype == 'proyecto' ) {
                		$clave = 'project';
                	} else {
                		$clave = 'new';
                	}
                }

            return $clave;
        }

    // Traducir la url en castellano o ingles, noticia o new
        function PostType_options_get_permalink( $url, $language ) {
            if ( 'us' == $language ) {
            	$url = str_replace( '/proyecto/', '/project/', $url );
                $url = str_replace( '/noticia/', '/new/', $url );
            } else {
            	$url = str_replace( '/project/', '/proyecto/', $url );
                $url = str_replace( '/new/', '/noticia/', $url );
            }

            return $url;
        }
        add_filter( 'msls_options_get_permalink', 'PostType_options_get_permalink', 10, 2 );

En el header.php llamo así al menu:

<nav class="menu_principal_departamentos">
                    <ul>
<?php
                        $terms = get_terms( 'departamento', array( 'hide_empty' => 0, 'parent' => 0, 'post_type' => 'proyecto' ) );
                        foreach ( $terms as $term ) {                            
                                $url = get_bloginfo( 'url' ) . '/proyecto/' . $term->slug . '/';
?>
                                <li class="<?php echo $term->slug; ?>"><a href="<?php echo $url; ?>"><?php echo $term->name; ?></a></li>
<?php
                        }
?>
                    </ul>
                </nav>

Y por ultimo en taxonomy-departamento.php:

<?php
	get_header();

	// IDIOMA
		$blog 		= MslsBlogCollection::instance()->get_current_blog();
		$idioma 	= $blog->get_description();

	// VARIABLES
		if ( $idioma == 'ES' ) {
			$buscar = 'BUSCAR';
			$ver 	= 'VER PROYECTOS';
		} else {
			$buscar = 'SEARCH';
			$ver	= 'GO TO PROJECTS';
		}

	// Saber por la url el post type
		$uri = explode( '/', $_SERVER['REQUEST_URI'] );
		switch ( $uri[2] ) {
			case 'proyecto':
				$PostType = 'proyecto';
				break;

			case 'noticia':
				$PostType = 'noticia';
				break;
		}
?>
	<article>
		<div class="pr_content">
<?php
			if ( $PostType == 'proyecto' ) {
				global $wp_query;
				$taxonomy 					= $wp_query->queried_object;
				$taxonomy->children 		= get_terms( 'departamento', array( 'hide_empty' => 0, 'parent' => $taxonomy->term_id, 'orderby' => 'id', 'order' => 'ASC', 'post_type' => 'proyecto' ) );
				$parent						= $taxonomy->parent;
				$not_the_last_subcategory 	= is_array( $taxonomy->children ) && count( $taxonomy->children ) && $taxonomy->parent == 0;

				if ( $parent ) { // Ficha Subcategoria

				} else {  // Ficha Categoria

				}

				if ( $not_the_last_subcategory ) { // MOSTRAR LAS SUBCATEGORIAS
					$columnas = count($taxonomy->children);
?>
					<div class="pr_linea"></div>
					<div class="pr_subcategorias <?php echo 'col' . $columnas; ?>">
<?php
						foreach ( $taxonomy->children as $key=>$subcategory ) {
?>
							<div class="th_subcategoria">
								<h2><a href="<?php echo get_term_link( $subcategory, 'departamento' ) ?>"><?php echo $subcategory->name ?></a></h2>
								<p class="th_subcategoria_description"><a href="<?php echo get_term_link( $subcategory, 'departamento' ) ?>">
<?php 
									$description = $subcategory->description;
									echo $description;
?>
								</a></p>
								<p class="th_subcategoria_gotoprojects"><a href="<?php echo get_term_link( $subcategory, 'departamento' ) ?>"><?php echo $ver; ?></a></p>
							</div>
<?php
						}
?>
					</div>
<?php
				} else { // MOSTRAR LOS PROYECTOS DE LAS SUBCATEGORIAS
					$taxonomy->children = get_terms( 'departamento', array( 'hide_empty' => 0, 'parent' => $parent, 'orderby' => 'id', 'order' => 'ASC', ) );
					$columnas  			= count($taxonomy->children);
					$current_category 	= get_query_var('departamento');
?>
					<div class="pr_subcategorias_menu <?php echo 'col' . $columnas; ?>">
<?php
						$term = get_term( $parent, 'departamento' );
?>
						<h1><span><?php echo $term->name; ?></span><span class="rotate1" id="down-icon"></span></h1>
						<ul>
<?php
							foreach ( $taxonomy->children as $key=>$subcategory ) {
?>
								<li class="th_subcategoria <?php if ( $subcategory->slug == $current_category ) echo 'activo'; ?>"><a href="<?php echo get_term_link( $subcategory, 'departamento' ) ?>"><?php echo $subcategory->name ?></a></li>
<?php
							}
?>
							<li class="clear"></li>
						</ul>
					</div>
					<div class="pr_mosaico e_categorias">
<?php 
						$loop = new WP_Query( 
							array(
								'departamento' 		=> $current_category,
								'post_type' 		=> 'proyecto',
								'posts_per_page' 	=> -1,
								'orderby' 			=> 'menu_order',
								'order' 			=> 'ASC',
								'no_found_rows' 	=> true // Si no hay paginacion, hace mas rapido la QUERY
							)
						);

						if ( $loop->have_posts() ) {
							while ( $loop->have_posts() ) {
								$loop->the_post();

								$pr_id 		= get_the_id();
								$pr_image 	= wp_get_attachment_url( get_post_thumbnail_id( $pr_id ) );
?>
								<div class="th_proyecto">
									<a href="<?php the_permalink(); ?>"><img src="<?php //echo aq_resize( $pr_image, 425, 217, false ); ?>" alt="<?php the_title(); ?>" /></a>
									<h2><a href="<?php the_permalink(); ?>"><span><?php the_title(); ?></span></a></h2>
								</div>
<?php
							}
						}
?>
					</div>
<?php
				}
			} else {
?>
				NOTICIAS
<?php
			}
?>
		</div>
	</article>
	
<?php
	get_footer();
?>

Funcionar me funciona todo bien, pero a mi detectar a través de la url en que post type me parece un poco chapuza, querría detectarlo de forma normal

Espero que se vea todo bien, saludos