I think there is also bubblewrap which flatpak uses, which can limit access to folders, and also XDG desktop portal which allows GUI applications to access file

I think there is also bubblewrap which flatpak uses, which can limit access to folders, and also XDG desktop portal which allows GUI applications to access files that are not available to them. Not sure if these are widely used though, iirc a lot of flatpak packages just have "normal" permission. Also, these are not very helpful for CLI applications.