When we see the old Madara talking to Obito after he was found, we can see that his right part of the body is destroyed and replaced with that artificial, Hashirama cells included "body", and we can also see that his face is in a pretty bad shape, too, but he's got his right Sharingan. How it happened, that his right eye came out harmless after that incident?
I think it's a plot hole. If you think that the Mangekyo was awakened for a moment, since we saw when he really awakened the Mangekyo, it may be a healing technique that he used to save just Obito's right eye, not his entire body. But I can't imagine his Sharingan being the savior because in that case Obito could have managed to slip through the rock with his entire right part of his body.