Perhaps the space-time jutsu that Tobi uses to pass through solid objects (Or send his solid body to another deminsion for a sec) was actually first activated by Obito, and allowed him to "phase" through the rocks that were crushing him. Maybe he "escaped" to that other deminsion and now is a former shell of himself only because part of his body/soul is still in the other deminsion. Kakashi should see if he can use his Mangekyo to send himself or another person to that deminsion and just see whats going on in there...or whos there...
Sasuke was there once...sent there by Tobi while fighting the 5 Kages. I wonder if he noticed anything while there....