> So if I am using a native nostr or web app with only Tor relays, and this app supports outbox, the privacy benefits are lost?

Well not entirely, as long as all your connections go over Tor, the clearnet nostr relay connections will go through multiple Tor relays and then a Tor exit relay before it connects to the clearnet nostr relay. It will probably look something like this : Your Tor traffic -> Tor relay -> Tor Relay -> Tor exit node -> clearnet nostr relay.