Afaik with molex your fan will be spinning at full speed.
With 3pin it depends whether the fan header is 12v or 5v. So at 5v your 12v fan will be spinning at about 42% of the fan rated speed whereas in 12v header, fan will be spinning at full speed. I think it also depends if the fan is 5v or 12v fan.
Edit: So if you connect a 5v fan into 12v 3 pin header, the fan speed won't increase as it will already be spinning at full speed.
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