You can route clearnet URLs over Tor but not tor onion urls ovee clearnet essentially. 

Mobile apps and desktop apps could probably pack a tor daemon in the app to route any onion url over Tor automatically. IIRC, Amethyst did this? Is that correct nostr:npub1gcxzte5zlkncx26j68ez60fzkvtkm9e0vrwdcvsjakxf9mu9qewqlfnj5z?