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.

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 the incident may be for his own good/enjoyment, or at the very least an accident ... (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.