I was using the flatpak version on arch for a while with no issues up until I started getting into modding and stuff. I ended up switching to the native version. Some issues were easy to fix by just granting permission to access a certain folder. Other issues I never figured out. Most importantly though, the vast majority of guides and tools simply don't assume flatpak which means that resources and community help is a bit more scarce. I think it is because of people that use the steam deck which is an immutable os that I was able to figure out anything regarding the various different things you may need to do in order to get different kinds of mods and programs to run withing the flatpak sandbox.