*Run him over* and *run over him* have distinctly different nuances for me.

*Run him over* has clear and malicious intent (to damage with a vehicle)

*Run over him*, absurdly, admits the possibility that it may be for his own good/enjoyment ... (a simple description of an action, without implied intent)


So, a 'bad guy' will try and run someone over.  A 'good guy' may run over someone by mistake.