Well I think they wanted to set out to make this as differant as a possible from a 2nd BD version which is why they didn't include the black shirt at first, and the bullet holes etc.
That doesn't make sense though, he was BD in the grey shirt, if anything, it would have been black only in this set, include a grey in a BD set and put the endo arm in this one like they've done and possibly entice people to buy the BD to get the spare shirt for a Cyberdyne mix.