It's not that they don't work better in conjunction, it's canonical's lack of moderation in the snapcraft store.

This could've avoided day one by adding a manual review process (like what they are temporarily doing right now)

I don't know how flathub handles new package submissions, but I think that they definitely need to have a process similar to what other distros have in place for native packages (heck, even Ubuntu's own repos have a review process)