After Carlo died Paul wanted to keep things smooth between him and Neil. Neil was the underboss BUT he was given more authority over certain crew. For example he was allowed to promote certain guys to captain in crews he oversaw i think. Of course Paul would have to approve gotti and angelo's induction but i could easily see Neil actually doing the ceremony since he had big power for an underboss. Gravano was apart of the white collar branch of teh family so it makes sense that he Paul was there to induct him