You are right, you cannot search in multiple bookmarks, but if the only bookmark a Wish-list book had was "wish-list," that shouldn't affect any of your other bookmarks or searches, as long as all the books you own also have a "books I own" bookmark. Then, to search your entire owned library, just search by the "books i own" bookmark. To search in your wish-list books just search by the "wish-list bookmark."
To search by a specific "Book" or "Recipe" bookmark such as "vegetarian" or "gluten free" search by the respective bookmark, and the search will still only show results of specific books/recipes that you assigned that bookmark. As long as you only place more specific bookmarks on books and recipes you actually own, it should not affect any of your searches.
It is certainly a little complicated, but it's just a suggestion for anyone who might be interested.