You can't select an item type as a criterion for a collection if it is not selected to be included in search results. In the "Search settings" (/@@search-controlpanel) you can exclude certain content types from being "searched and be available in the user facing part of the site". That actually corresponds to the list of types_not_searched in site_properties. Now that list is excluded from available content types as a criterion for collections.
Plone has multiple ways of excluding a content object from the navigation:
idsNotToList in portal_properties/navtree_propertiesmetaTypesNotToList in portal_properties/navtree_propertiesThis works fine but the item is still displayed in the navigation tree if it's the current item (the one you're currently viewing). This may have a reason (usability?) but it is not what I want in some cases.