Bazzite lead developer here, we actually never used the flatpak. Our first release had it installed in a distrobox container on the desktop images. Deck images always had RPM Steam because Steam is essentially functioning as a desktop environment there. We moved them both to be RPM for support consistency reasons.
For that, check out Bluefin or Aurora. They’re all under the same umbrella as Bazzite, but with a user/developer focus instead of a gaming focus.