I don't know of any PWM fans that have 4pin 'molex' connectors also so we'll just assume the usual Nexus-like 3/4pin configuration.
there wouldnt be any voltage differential across the lines,
If a fan is connected to the mb sysfan (of which most? are speed controlled), then there could be a difference. The mb would be sending say 7v and the fan 4pin from the psu would be sending 12v on the same wire. If I knew more about electronics I'd probably know the outcome. I do know that a fan connected to the 3pin sysfan on an ASUS 690G worked for a couple of hours and then didn't (I might
have been trying different fans without cycling power). The other two, CPU and PWR, worked fine. No other fan would work so had to rma it and the replacement has worked for a while now. Granted it might have been a cold solder joint.