Just my 2ct on the situation:
The fix edits the default.lua control scheme, wich is an insanely useful thing to know how to do in general esp if you're not fond of Target.
You could essentially make any switch a 2 or 3 way "Special For Joystick" switch by modding that.
BUT!
It might break some functionality for solenoid / spring loaded switches that are supposed to return to position but you just hold them in place with your HOTAS.
(Witch is actually the case for the AP switch, it flips back if the AP turns off!)
Thinking about it, that really explains a lot! I had some very funky behavior when leaving the AP on and going off course in game:
It would trip the AP to turn off, but the TM switch held it in place so the game would treat it as if it got turned back on making me flip-flop around with the AP stuck in an on-off loop.