I went a step further and have user-installed flatpaks with a custom flatpak directory so everything installs on a separate small hard drive. If the whole system goes down (usually due to my testing things!), I can reinstall set up the custom flatpak and everything works again. In theory. But it borks inter-flatpak communication (flatseal cannot find any other flatpaks and is thus unusable). I moved over to distrobox (which has its own issues, but works better for the OS wiped/reinstall scenario).
In that case you should use user-install flatpaks and separating and reusing your /home partition
I went a step further and have user-installed flatpaks with a custom flatpak directory so everything installs on a separate small hard drive. If the whole system goes down (usually due to my testing things!), I can reinstall set up the custom flatpak and everything works again. In theory. But it borks inter-flatpak communication (flatseal cannot find any other flatpaks and is thus unusable). I moved over to distrobox (which has its own issues, but works better for the OS wiped/reinstall scenario).