Instead of bluntly blocking things why can’t Flatpak just simulate a full environment and just prompt the user whenever some application wants to read/write to file / unix socket at some path?
Because the user getting a hundred popups on app start for various files the app needs isn’t exactly a usable experience. Also, blocking the app’s main thread (which is the only way you could do this) is likely to break it and cause tons of user complaints too.
Aside from apps using the APIs meant for the purpose of permission systems, there’s no good way to make it work.