Flatpak doesn’t have an “ask for permission” system afaik, at least not standardized.
Exactly, and that’s precisely the reason why it’s still not a viable solution for the average user. This a big problem and a problem of consistent and integration between Flatpak , GNOME, KDE etc.
Get them as big as possible (wallet allows to), because you’ll get quickly annoyed at having multiple smaller drives. You’ll have to deal with more space, more cables, more power, more sata expansion, more heat etc.