Are they essentially 4-separate channels of controller setting generating their own configurations files?
Yes, they are separate as Bizman said.
If the "Auto select mode" checkbox is checked, the stick map mode you've programed using the controller's drop down setup menu for the (1)fighter, (2)GV, etc will be auto selected to match use. This happens even if every button and axis is set to None.
If you're using VR, do the setup while in the tower only and don't go to a plane while in the controller window. Maybe this will be fixed soon.
Be sure to backup your controllers' .jsm files and set Protected once you're done with the setup.
If you're editing the .jsm files directly, as in copying the nonVR version to the VR_ version, don't overwrite the first two lines!
This is particularly useful if you GV for using a button to accelerate, slow, jump to gun, or commander position.