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.