I read the 3 pins are for charging and notifying the phone that it is plugged into the dock so it can start the Bluetooth on the phone. The phone then communicates via Bluetooth to the dock and sends audio to the audio jack on the dock (the real GSM style dock that is).
The link below is to a thread about an inductive charging hack that uses these pins. The only problem is nobody knows how to convince the phone is can fast charged with the 3 pin connector. If you connect +5V and Ground like the hack shows it will slow charge.
http://androidforums.com/verizon-galaxy-nexus/461891-verzion-nexus-car-dock-3.html
your link just links back to this same thread.
