2 issues i see
1) your not connecting up all the 12V lines. there are total of 5. so it may still pull power from the motherboard.
2) path of least resistance...  between getting power from motherboard or from the molex connector the difference in resistance is very small.
possibly measurable in milliohms. so it may still pull power from the motherboard.

I'm no electronics technician so i can't say for sure.

but i do know that hen i physically cut the ribbon wire and plug the 12v wires into a molex connector i am for sure not drawing any power from the motherboard.