Okay, I went and read BobRob's instructions and figured what he's talking about.
It seems that whatever board he is using has continuity between the top and bottom +12V pads without the JAMMA connector attached. Knowing this, he can use the 2nd +12V wire as an output to the coindoors to supply the +12V for the light, meters, etc. I believe all JAMMA boards are like this but I would check to make sure your boards have the same continuity betweeen the top and bottom pads of the edge connector, and if so, do it just like BobRob says, if you want.
He only does it this way because he wants to keep it neat and not run a wire to the coin door from the power supply. The only concern is that +12V goes to two pads on the board to ensure a good connection with the +12V source. It is a lot less unlikely to lose contact with that source with two contacts instead of one. If this concerns you, you can either solder-attach a new wire to one of the +12V wires near the connector and send it to the door in the bundle, or just run the +12V to the door from the power supply.