The difference is mostly cosmetic, but they really go beyond just the physical appearance. I am a fan of the small things like when you change the abilities with the Chapter Master. Because I went with Dark Angels, I hear "Repent. For tomorrow you die."
As for the favours on the barges, I have only been able to afford one so far. My primary barge I gave Chapter Master, and the other will be receiving Master of the Forge. When I'm getting into 700pt games, I am running twin Battlebarges, and so far have only lost against Eldar. Although I think I might change the skills on my second barge to include the sensor array that you can attach to an enemy ship. You need them identified to be able to fire the homing boarding torpedoes, and they are too fast and can usually make it into a gas cloud easily.