They are hooks that latch on the common GUI application library calls for things such as "open file dialogs" such that exeptions to the sandbox are implicitly added as-you-go.

They cannot prevent for example direct filesystem access if the application has permission to open() stuff, like if they're not running in a sandbox, or if said sandbox have a "can see and modify entire filesystem" exception (very common on your average flatpak app, btw).

E.g. under X you can use bubblewrap or firejail to restrict access to the web or whatever for some program, but still give that program access to for example an xdg portal that lets you "open url in web browser" (except the locked-down program can't for example see the result of downloading that web page)