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You could add an ability to the colony component to reduce ship maint to counter that I guess.
If you do that, then what's to stop someone from making a Baseship with a colony module on it and getting low maintenance fleets? You should increase the size of the colony module by 600 kilotons and the colony ship by 620 kilotons and give the colony ship itself reduced maintenance. That way, you couldn't stick the colony module on a small war ship, like a light cruiser, to get a fast colony ship. The extra 20 spaces would allow more room for accessories like supplies, solar sails, cargo bays, etc. With huge colony modules (800 kilotons), you could still put one on a baseship to get a high initial population, but it would be slow and high-maintenanee.