The core design has only one real colony module. The other one is purely cosmetic.

Also note that you can place a colony module and a troop module on the same ship and that ship will be able to colonize empty planets as well as conquer enemy planets. So if you have Planetary Invasion and Advanced Troop Mod you can have a 1.25B colony ship which coupled with max pop growth tech and abilities gives you a colony that will become profitable in three turns (assuming reasonable levels of economic ability).