That's OK with me, and maybe, just maybe, XD002 might come thinking that Team Galactic are trying to mimic what Cipher did before. Although at first, he might believe that the player is working for Cipher, and will fight him/her. But, when he loses, the player tells him that he was mistaken, and then XD002 might help him/her during the final stages of the game. But I don't mind if XD002 only makes a camo appearance right at the end of the game.
Besides, XD002 has experience with Shadow Pokemon, and these fossil Pokemon are just like Shadow Pokemon. So it would be fitting for XD002 to appear, even if it's as a camo.