If you are making your own distro, creating your own flatpak store is trivial, that's all what matters. Linux Mint doesn't use snap exactly because Canonical forces everyone to use their snap store.
Canonical doesn't force anyone to use anything. Snap is open source, just modify it to use a different store if you want. Mint literally forked a zombie DE, but changing a few lines of code in snap is an issue...
Defaults matter a lot, snap is not open source (client is, backend isn't), you cannot "just modify it (Ubuntu)" to use a different store, because Ubuntu installs snaps even with apt. Mint is not part of the discussion.
