Yeah, definitely an advantage to have most of a ship "not available" for exploring because of damage.
I was pondering how a mi-go would transport oon around and settled on a ship, especially since the mi-go can fly through The Void.
It's probably reasonable to have the oon in a bag or something that negates their mass and just fly them there, or even some teleportation or other weird science method.
The only weird point is having the mi-go escape in a capsule but it is really a McGuffin. I wouldn't want to face a mi-go with a laser pistol. Save vs death or disintegrate is no fun, but hey, don't poke the mi-go in stasis.