My Gigabyte UD3 board automatically recognized 3 or 4 pin fan connections and applied the required control for what was plugged into it.
I ran a hyper 212+ using a 3-pin splitter that only had three wires for one fan and two for the other.
basically, the motherboard only "saw" one fan and applied voltage control to that fan. The other fan simply got whatever voltage was sent to the other fan.
Both fans worked, and the motherboard never knew the difference.