My issue with flatpaks is that having too many flatpaks becomes a chore to manage. I did not have a fun time with Steam in a flatpak (required some mucking around to get the DPI and cursor size right) and same with Chromium a while back (took me a long time to figure out how to pass on the flags to enable Wayland support). IMO, having a single container (or a container for a particular activity, like gaming) would be a much more cleaner approach, while offering the flexibility akin to a mutable OS (so no weird flatpak quirks to deal with… in theory). This would also make things like backups easier, I could just save my “gaming” container to one tar and not worry about whether I missed any dependencies etc.