so, after some digging about, it looks like the docking mode is set by the middle pin.
from digging about in the sources, I have found board-tuna-pogo.c which is the file that configures a GPIO pin to be used for the pogo functionality.
It looks like when first connected to a dock, the phone sends a wake up pulse of 100mS, then waits for the dock to respond with a similar pulse back to the phone.
The duration of the pulse is what sets the dock mode.
Here are the times from the sources(times are in mS):
#define POGO_ID_CARDOCK 100
#define POGO_ID_DESKDOCK 200
Going to try a couple of things to test this on my real phone