Perhaps you are over thinking it. How about a player sided flag that checks for the entity name and disables Drive Assist and stopping on signs when you get in the aircraft akin to pushing the Drive Assist button? You can have a list of modded aircraft names. There really aren't that many aircraft mods in factorio. :)) And if people make aircraft mods, you can have occasional updates that adds the aircraft names to your mod. More over if you are in the aircraft and manually enable Drive Assist by pushing on the button it will also stay on the next time you get inside that vehicle. ;))
Not at all. Checking if a vehicle is airborne is super easy. Creating a list of such vehicles is super easy. You simply check the collision mask - worked like charm for both an aircraft mod and helicopter revival one.
Finding all the right places to plug in those checks is a bit more complicated, particularly if you do not want to break existing savegames, or if you want to maintain sane state that the mod keeps internally when the setting is turned on or off in the middle of the game. This can get further complicated if you are in a multiplayer setting. Or if the player decides to toggle the setting while sitting in a vehicle on top of a sign. Or if a player decides to toggle the setting while driving the vehicle that has had its speed limit capped off by speed limit sign.
It is not necessarily super hard, but there are corner cases to think about. And some of those checks do not necessarily fit in nicely with the existing code (like you just change 1-2 lines in the code).
Best regards,
Branko