One point of difference I feel is worth pointing out:
From a narrative perspective, saucer separation on a Galaxy class and MVAM are fundamentally different in a way that I feel should be reflected in the rules of using them.
On a Galaxy class, saucer separation is meant as a contingency thing, not as the ship’s primary operational configuration. So I think the rules as they exist make sense (two ships at -1 scale).
But MVAM is not a contingency thing on the Prometheus, it’s supposed to be a benefit - something above and beyond what it can do in normal one piece operation. So I don’t think the three ships at -1 scale necessarily makes sense in that context.
If I were using it, I would probably set it up something like this:
It’s still considered one ship, but gets some benefit to its attack and/or defense. Maybe it gets to fire a weapon twice in one turn instead of once (three times in a turn would probably be too much). And/or hitting the Prometheus is +1 difficulty while in MVAM.
Any breaches the ship takes get consolidated into the one stat block, but the more breaches the ship has, the more difficult it is to reintegrate (and may become impossible with enough breaches).
Just my two cents, my campaign is set well before Prometheus would come into play, so it’s not an issue I’ll have to deal with personally.