> Can't say I've stumbled upon a lot of desktop apps (not terminal utilities) that are not on Flathub.

Perhaps you just don't use that many things that aren't really popular or well known? I can't find PuTTY and KeePass (though obviously there are alternatives in those cases), applications that both have Linux versions and that I use every day (and aren't even that unknown).

Also, unfortunately the limitations of Flatpak mean even if what you want is there, say Wireshark, it often won't have full functionality because it is impossible to give it the permissions it needs. In Wireshark's case, it can't actually capture any packets. If you want to actually use it you'll still need to resort to a different installation method.