After a friend of mine showed me how the MVAM worked, and the stats, I had an epiphany. Why not allow those who have aquired both the Tier 5 refit exploration curiser equip the MVAM. When selecting the Alpha mode, the player controls the Saucer section, and the stardrive section acts as a beta pet. If the player selects either Beta or Gamma, the Saucer acts as a Alpha Saucer. In any case, there is only one pet, and it doesn't ever act like a Gamma pet. If it is tweeked, the only major difference between equiped and not equiped would be choosing the role the ship plays in combat. MVAM would still be most effective on the Advanced Escort, but would give more flexibility to the Galaxy refit, and allow a third ship that could use the item.
This actually seems like a pretty good idea. It would also make the MVAM more of a worthwhile buy, especially if you are currently running the galaxy.
A possibly tweak could be, if you equip the MVAM to the galaxy, it launches a shuttle as the gamma pet, which delivers support like the tal'kyr support craft. Plus it would be fun to select the gamma pet and flit around in a shuttle craft while your pets deal damage. If you fly the shuttle, it should get the jam sensors ability, to avoid being targeted by bigger ships.
Technically speaking, most ships in the st universe are supposed to detach like the galaxy class. Even the Klingon pods at the fron were supposed to be able to seperate. There would be exception, like the Miranda class and such.