I doubt either side would be restricted of colors, that would take away from the extensive customization. It be a condrictory if you could get oh so many security outfits but can only color them in green or blue. I'm more than certain you can color your characters in whatever color you choose,regardless of which faction you are. I have yet to see any game, bad or good, popular or unheard of, that would not allow colors for all teams
You obviously missed Transformers: War for Cybertron.
Which had designated colours available to each side, then you could adjust brightness and contrast within the available base colours.
Decepticons for pinks, purples, and the pastel-shade colours.
Autobots got the primaries and vivid colours - Blue, Red, Yellow, Orange, etc.
Basically, the Autobots get vibrant colours, and Decepticons get more subdued, subtle colours.
Made characters both visible against he background and distinct from enemies.