My guess is that many options work by capturing the active player, and apparently the game works in such a way that it makes an AI player an active player while running its turn. So if the options are activated while the AI plays a turn, the trainer isn't able to discern that it's a non-human player and works for the AI just as well. I don't think it's possible to write around that, so we'll just have to remember to turn the options off before ending the turn.

Hypothetically, is it possible to capture the event relating to a user clicking End Turn and auto-disabling the options then?