The Macintosh version of the FlightStick had an ADB (Apple Desktop Bus) plug that had a port on the other end so you could plug in another device. It’s been 30 years. Do you think I might misremember? Maybe it was a FlightStick and a Saitek joystick? If you are running the original game on period hardware and tell me that the software wouldn’t know how to tell two different joysticks apart regardless of which type, then I guess I’d have to admit that there’s something fishy with my memory.
look into "period hardware" which is itself a "dual joystick" (typically literally sold for use in descent). it's a gimmick that sold i.e. why have one joystick when you can have two. Then you should just have a single i/o interface to your MIDI game port.