My understanding from watching the little bit of available footage shot by the men who discovered his body is that Mallory's head was buried under the loose shale. You see the same thing with one of his hands/arms in the footage. The researchers have to scrape loose rock away before they can investigate.

In the pictures you can see that the shale directly above his shoulders is raised, like it's covering something, and there's a bit of something brown or yellow just visible peeking out from between the rocks.

As far as the holes in his body go, I don't have a strong enough background in forensics/biology to guess but it's probably related to the extreme cold and the length of time he's been there. His body is effectively mummified.