Well, many of the parts that have the same model but different colors in the part menu actually DO paint differently, especially regarding the armor pieces. It's to the point that I actually made a template creature to help decide what parts I wanted to choose due to how they would end up painting. That being said, sometimes the differences are tiny enough not to notice right away.
Note: A lot of things in Dark Injection look odd in the editor but come out fine afterwards, such as the invisible limbs being visible, and the spheres that hold the effect/ability/voice parts being visible. Another thing you may notice is none of the custom abilities work in the editor, but again, in game play they function properly.