Yeah, a heavily-damaged ship, drifting above a habitable world, acting as a defense for a colony, I can see. Some or most might even try to stay aboard for a while, hauling resources up, but eventually, as tech dwindles, even if intellect doesn't, the air scrubbers will deteriorate, water purifiers fail, foodstores deplete, the plasma genetoria will go dark, and the ship will die. The fact that the ship CAN go to other places for resources, and HAS to, sort of make it not a colony for me, not including also not making anything. Also, while you could certainly pimp your ship(s) out to bypass my limitations, that seems a spendy way for a Rogue Trader to go about making a colony. A ship that moves is much more valuable hauling my cargo, fighting my enemies, or taking me to the next beautiful woman, money-making gala, or long-lost ruin, choked with archeotech I can pilfer. Look at the Light of Terra? It's sort of a "colony" of savages and benighted degenerates. that took 2,000 years, and the ship is next to dead.
One interesting note here is that colonies do require a big influx of resources (represented by the hit to profit factor) that comes from needing a lot of technology, colonists, wages, and long-tail infrastructure. This is, oddly enough, most of the stuff that ships have already accounted for in their upkeep and purchase costs.
I can see a large transport ship being a traveling colony. It would require upkeep, sure, and shipments of resources that it needs; but it could act as a mobile manufactorum complex able to build whatever other colonies need. It could also be a mobile refinery, or repair facility, or research base, or Ecclesiarchy outreach post.
That way, your ship would be generating products/services that make profit and require mobility.
Size is still a question, but going through an endeavor to purchase more ships, or build additions to the ship, or turn the ship into a void station could all be methods to get around it.