It shouldn't have to be. Hell, you can even give Noctua fans badtouch and control their speed via voltage instead of PWM duty cycle.
I'd guess that the Noctua fan is drawing more current than the GPU is willing to push out on the +12V pin/rail.
Worst case, you can use just pin 3 (RPM/Tachometer) between the GPU and Noctua fan to report speed, but power the fan (+12V and ground pins) from SATA or "MOLEX" power from your PSU. Hell, there are even little fan voltage -> fan PWM converter things out there than you can stick in between w/e the GPU is trying to give on its +12V pin and the Noctua's PWM pin