Basically the ship fabricates a colony/transport module from old comet parts and interstellar dust 
Thereafter, you can always add pop the usual way, by landing on a planet hex and then moving off.
Yor should be able to upgrade to a populated transport: they just build new Yor as part of the ship walls. Bonus: the ship would not need any doors or intake ports, which should give an armor bonus for being hermetically sealed. They build the crew inside-out 
