I recently got rid of my MGCD but I can tell you that the device works best and support the added features better withy NAOMI based games. The MGCD natively will support the JAMMA std for action buttons so 3 is your max without altering your harness, etc. Here is the pinout info for a couple more buttons:
A4 - Y Button
A5 - Left Trigger
A6 - Right Trigger
It should work basically in theory, but depending on what the controls are like for Jedi Power Battles it may work better if you were to not use the controller portion of the MGCD and go for a couple of hacked Dreamcast pads.
Hope this helps
-Goz