If you don't use TARGET at all, then the Joystick, Throttle, and Pedals, show up as individual controllers. You can use them as such.
Without TARGET, I loose a great deal of functionality I have grown to appreciate.
I've never tried to use the TARGET GUI, but it still combines the three controllers into one virtual controller, witch will be considered by Windows as a single controller and restrict the number of axis.
So if you are interested in using TARGET Script Editor with all three, look at this thread:
https://forums.eagle.ru/showthread.php?t=218932