Colony ships aren't military transports. To build a military transport you have to research the "Planetary Invasion" tech - after you have researched "Galactic Warfare" and "Space Militarization".
Well, you're right. The custom races are given less abilities. This because pre-made races have 10 "free" ability points plus other points that are already given by default, while custom races have only the free ability points. You can give more ability points at custom races by modyfing the "RaceConfig" document in DA/Data/English. Just change the "15" in 15 (under the custom race "options") with another number of CP. I have given my custom races 25 CP,
