Well, even bleeding in the brain is not necessarily immediately fatal. I take that phrase to mean that, left untreated (as it was), she would have succumbed to the injury if something else yet undiscovered did not kill her first. You know, like strangulation. Or a blow to some part of the body that isn't accounted for yet.
No, you should not assume her brain was inside her skull. Part of the skull was at his house, the rest was in Logan Canyon. In between her death and ending up in Logan Canyon, she was burned (apparently twice). Brains are pretty liquidy/delicate.
You could read it this way: someone dealt a death blow to Kenzie, by hitting her on the head. She could have been run over by a car after that and they don't know. But she would have died anyway.
What might be inside the skull are tell-tale signs of the degree of brain damage. This might require microscopic analysis that may or may not have been done at this point in time. What the coroner can confidently say is that she was dealt a death blow and obviously, did not receive medical treatment. She could have had multiple other soft tissue injuries that have now disappeared.