CRAU characters are brought into the game via the same mechanic as other characters, only considering the previous game to be the universe they're taken from rather than their canon! As such, changes they experience in that game should remain, as well as any fundamental changes in their physical form as dictated by that game's unique setting.

In respect of Systemwide specifically, this means CRAU characters brought from there to Ataraxion would be taken in their Real bodies, rather than their Matrix ones!