But I don't see why removing the pins from the docking connector would require me to terminate them ? If the player is in "home mode" and a serial cable is connected to the player, then those pins in the docking connector are also not terminated (I think), and it still works. Or am I completely wrong here?

Fear not, for I perceive that it is I, Jim, who is suffering from the dreaded brain fart!

Yes, no reason why you couldn't preserve the serial connection on the back of the unit. I was just in a mental muddle.

I thought about subverting the serial connector pins for digital output but then decided for some reason that I still want permanent serial connector on home docking station and a connector for GPS whil in car...