Same boat. As a user, I greatly prefer everything to come from the repos. However, as a distributor, Flatpak makes so much more sense.
The only Flatpak I have installed is pgAdmin. I looked at the build on Flathub with the idea of porting the package myself but got scared off. It was a maze of Python dependencies running in Electron. That seems like exactly the kind of thing that may be better off in its own sandbox.
Does Sea of Thieves work on Linux? I thought it had kernel anti-cheat.