First, I must say that this is a great guide for setting up controlled radiator fan though motherboard.
Second, thanks for pointing out native 1080 ti capability to control PWM fan. I have connected a good PWM fan to the connector, and now, I can control it with the GPU slider/curve in Precision.
To the right of this connector there are two more PWM connectors. One has both the pump and the radiator connected to, and the next one is connected to onboard fan. Thus, EVGA should have used one to control a PWM radiator fan, one for controlling PWM pump, and the last one for controlling the On-board fan. I am not sure why EVGA did not do this. I suppose, they want us to buy the full hydro, but it is a do-it-yourself setup, which is even more involved than changing a fan in the hybrid version.