Obviously, the Enma powers of the Rinnegan can put back a shattered body, and it could also manipulate souls.
One lesson I have come away with is that it is unwise to leap at a possible outcome even if that outcome appears rational and feasible. In other words, just because the Madara=Obito theory is now possible based on established Maga facts, that does not mean Kishimoto will go that way. In fact I sometimes suspect that Kishi purposefully avoids a storyline, just so as to bamboozle fans, never mind that he himself constructed an eight lane concrete super-highway leading to that storyline in the first place.
The point I most wish to make is this, if Madara turns out to not be Madara in Obito's Body, it won't be because it was outlandish or unsupported by the facts, it will be because Kishimoto at some point decided not to use that option, having created the possibility for that option in the first place, and knwing full well how much debate it has generated with fans.