Flatpak is awesome, I love it so much. It lets users pick a distro based on the unique features that distro provides, without having to worry about whether their favourite apps are packaged. Since you’re considering switching to debian+flatpak, here is a list of pitfalls I’ve run into in flatpak so far, maybe this can save you some troubleshooting:
You need to have a thing called an “xdg dekstop portal” installed. Otherwise filepickers will be broken. On Debian this should be a dependency of flatpak, so it should be installed by default tho.
If you’re manually restarting Xorg without using a display manager, make sure the xdg desktop portal process doesn’t get started twice. Otherwise it will be broken
As far as I understand, there’s no way to use xdg desktop portal to forward an entire directory through to a flatpak’d app, unless the app itself asks specifically for a directory. So stuff like opening a .html file that references a .css file in the same directory with a flatpak’d browser will be broken, unless you manually make an exception using Flatseal or flatpak override.
Make sure your root filesystem is mounted with “shared” propagation, otherwise umount commands won’t propagate into flatpak’s sandbox, and drives will get stuck in a weird state where they’re mounted in some namespaces, but not others. This should be the default in Debian tho.
If flatpak’d Firefox has ugly bitmap fonts, follow this workaround
Anyway, this is just my experience running Flatapk in Void, hopefully it works smoother for you on Debian.