brah, it is not a flatpak issue, the same happens with the portable version i.e. the one you'd get via deb/rpm/whatevers. it doesn't accelerate video under wayland but does with xwayland; If you got a commensurate rant towards wayland, ixnay please.
as to why flatpak at all, I like my system stuff and my application stuff separate. thus my apps are all flatpak and autoupdated via systemd timer (another rant?) whereas my system stuff get updated like once a month or so as I hate rebooting.
I'm sure you found by now that your use case doesn't match everybody else's, so chill with the absolutes a bit.