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For, in the final analysis, our most basic common link is that we all inhabit this small planet. We all breathe the same air. We all cherish our children's futures. And we are all mortal. - JFK
My personal 'solution' to the question 'why use colony ships' was to make the colony module much more expensive and then give colony ships a maintenance reduction like bases. So, yes you can put colony modules on other hulls but it's a heck of a lot cheaper to use actual colony ships.
In one game I put all three types of colony modules onto a baseship so that it can colonize any planet, but it was too expensive and slow to build them so I stopped doing that.