What about cloaking devices on ships that have colonization modules? Can a planet be colonized by a cloaked ship or would it have to decloak first?
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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.