Actually if you set up the pin connector correctly you should be able to use controllers that have the d-pad and buttons on a different ground. For the connector coming from the arcade pad, set it up so that the grounds are separated. So you would need at least 13 pins: 4 directions, 6 buttons, start, 2 grounds. Then on the connector for the controller in the project box, if it uses a single ground, connect the two pins with a wire and then run a wire from one of the two pins to the ground on the controller’s PCB.
Although doing it this way you have to assume that all the controllers that use two grounds have them set up in a single format, such as with just directions on one and just buttons on the other. I dont know if this stays the same or not, but if it varies slightly then you may need to break the grounds up into 3 or more pins and just connect the pins accordingly when you make up the project box connectors.
As for drilling the PCB, just a regular drill bit would be fine, preferably the smallest one you could find that will still fit the wire you are using. Although I wouldnt recommend drilling it. If you drill it and then solder you have to make sure to test everything out with a multimeter to make sure that the wire is actually making a connection with the thin copper plate in the PCB.
I tried this on an extra piece of the PCB for the L buttons that I had left over from my controller. It seemed to make it easier, but then when I tested the connections, one of them wasnt connected right and if it was the real thing I would have to spend extra time messing around to remelt the solder and reposition the wire and so forth. So I would stick with soldering the wire right to the PCB rather than drilling it.