I wanted to play the game with a joystick, keeping in spirit of the arcade experience. I also had the reversed lightsaber battles.
In order to have inverse joystick controls and proper lightsaber control, I only set JOY Y AXIS INV, and leaving the service menu control at up>up, down>down. I didn't needed to change the cabinet style from DX to upright, but I did turn off the feedback lever.
Now I have flight style cockpit control and correct lightsaber control. I did have to initially use the mouse to bring the crosshair to the center of the screen (it was at the far right) but once I did that, the crosshair starts at the center, even with reboots.