im nobody official but you could fit alot of people if they where asleep and stacked in beds for the whole trip...: I was in submarined ANd we fit 30 guys in the space of two large walk min closets for berthing......so if it ever bothered me..which it didnt until now
thats ghow i would explain it.
whole invasion/colonization force is asleep for entire trip except for small navigation and maintenance crew.
or maybe they are actually empty and just hold the genetic material to immediatly gestate a billion humans upon completion of the journey.....dont think theres enough time for that based on the fact you have a working colony almost immediately.
just some ideas...to me filling in the canonical gaps(if this is one I'm unofficial) is most of the fun o ngames like these. Thanks stardock for a great game 