Chiming in to report that it still does not work (AAI Programmable Vehicles). AAI's GUI for programming a vehicle in the top left corner of the screen is gone and you also can no longer select those vehicles with the AAI unit controller after you load it onto a wagon and then unload it. This includes vanilla and modded vehicles since AAI adds the programmable stuff to all vehicles. It basically removes the AAI mod from the vehicle and they're back to vanilla after unloading from a wagon.
Picking up the vehicle into your inventory and placing it back down fixes the issue(until you wagon it again of course).
Reloading a save or exiting the whole game and relogging does not fix the issue.