The disconcerting part of this whole deal is that across the US, police are in the habit of “knee dropping” on face down prone suspects. I winced when I heard the type of injuries he had sustained, because that is similar to what could happen with a knee drop.
What matters right now is that “unexplained stop” the paddy wagon made. This might have been the timetable, and there are few facts backing up this theory:
1) Police arrest him, reporting that the arrest was “without incident”. Typically if police are aggressive, even if the suspect is not resisting, they will scream “stop resisting!” several times. This is so they will have a fallback charge of resisting arrest.
2) Inside the paddy wagon, the perp starts throwing himself around, much like a drunk will sometimes do in a police holding cell. This is when he likely got the head injury from a bolt head on the rear door.
3) The police make an unplanned stop to go into the back to restrain him. In the process one of them does a knee drop on him, breaking his neck. Immediately stilled and unconscious, the police decide to transport him for medical care. But do not give him any aid, because at this point it would look incriminating.
It also seems possible that the cops were accelerating and slamming on the brakes, to toss him around in back and shut him up.