It is important to remember that neither Groody nor Baumgardner said anything about the issue on the day of the examination. It was only several days later when the two men were discussing the event that they became suspicious. And they knew that the skullcap should have fallen off in the coffin before anyone touched it. Not only was the skull intact at Baylor, almost all of the scalp had rotted away, leaving no visible mark. This passage is an extremely revealing one.
Series appear above.
But it is a different thing to say the skull was intact and to say there was no craniotomy. They did their jobs and left, presumably in an expeditious manner. In the process the bottom of the vault fell breaking the vault causing the casket to deteriorate to a degree. Whoever caused that is the same faction that caused the assassination in the first place. In my mind, a cover-up had taken place.