The fact that Flatpak supports multiple repositories whereas Snap only works with Canonical's store. This is because the open-source Snap utility on your Ubuntu install doesn't support adding other repositories; and the server it talks to is closed-source and undocumented. (Oh, and don't get brilliant ideas with DNS redirection in your head, there's digital signing, which means the only way to get Snap to accept other Stores is with a full recompile.)

As for Flathub itself, it's like the Snap Store... but you aren't locked in, and the backend is open-source, and it's not directly owned by a distribution maker (even though it is definitely closer-in-kindred with the Fedora Project), which makes it far more palatable to people with even a modicum of understanding of the Linux and FOSS philosophy.

I harassed them nearly 6 years ago about this. https://forum.snapcraft.io/t/external-repositories/1760