If body paint works about the same (at least conceptually) as deep paint 3D it must be great!. I LOOOOOVE deep paint! It's awesome! Works just fine on Milennium figures, and everything else I threw at it so far.
You paint with photoshop like tools, directly on the 3D model. It's simpler to use then Zbrush, especially if you used photoshop in the past.
I haven't seen it do anything odd with multiple groups (material or polygon groups) on the object.
Well, I hope you guys didn't mind the digression into Deep Paint here :)

Hi, my namez: "NO, Bad Kitteh, NO!"  Whaz yurs?
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