I _believe_ it's related to the DirectInput inteface in FSO. It only reads how Windows containers the input device, regardless of what the devices software or drivers have to say, because those ALL go through the windows implementation layer. They have to.
Ex: My Saitek X52-Pro reads the same way. And aside from the slider on the throttle, everything reads properly, including twist. Though, by default, the "Twist" function is not associated to anything, I have to assign it directly. Same with the Throttle.
FSO (and by extension, the Launcher) at the current moment will always read based on the OS reported layer handler. This may change in the future, but I can assure you that so long as it listing that device, then it has detected that there is a Joystick attached and that the rudimentary and basic functions of it will work correctly, even though it's not "properly" reporting the "correct" device.