When the rocks caved in the ceiling of the tunnel, Obito's body fell away from the rocks. Hence why the rest of him wasn't crushed and why Madara called it a miracle.
If we assume that he used his MS abilities, then he would be at the bottom of the rock pile, just not crushed since he'd be still "phasing". And Madara would have had to dig him out.
He did not use MS. He still has 2 tomoe sharingan.
And there you have it. Good day.

If we assume that he used his MS abilities, then he would be at the bottom of the rock pile, just not crushed since he'd be still "phasing". And Madara would have had to dig him out.
He did not use MS. He still has 2 tomoe sharingan.
And there you have it. Good day.