Really interesting article about default directories and non-default ones.
For flatpaks you can easily restrict their access using such referenced directories, but they seem incomplete by default.
Some ideas:
smb shares using gvfs or kiofuse
/run/media (to avoid host)
this is of course only applicable to static file permissions, but I dont see how every app adopts portals in under 5 years. Also, many workflows seem broken with portals.
This forbids some, allows some others by default. I am not sure if this is the correct way to do, and some xdg-dirs are still missing.
Also, what about /run/media/user, I couldnt find any xdg-dir while that is the location that is used rootless with udisksctl, which I suppose is also some kind of standard.