Alien 3 is a very different situation. There is no "Director's Cut" of that film in any state, and the Assembly Cut was part of a big push to sell a box set back when mainstream audiences actually cared about things like box sets and special features.
If Ridley wants an alternate cut of
Prometheus, he has (well, had, pre-Disney) the pull to do it. He likes the theatrical release. Bless you, Ridley, but uhh, even most of the alt. takes that were actually included on the disc were better than what we got in the final film.