I don't think the faction-specific method will actually work 100%. theother has shown how I thought we'd need to set it up and I'll use that to explain what I believe the problem is...

I think it can now be accepted that while autocalcing only checks the triggers once, player-fought battles check them twice and that all AI vs AI battles are autocalced.

Using theother's handy example, while considering that similar changes will be needed for BadCommander, let's consider possible battle outcomes...

AI vs AI: The winner gets a point in GoodCommander and the loser gets a point in BadCommander. This is the desired result and is in effect the baseline to which we compare player vs AI battles.

Player vs AI autocalc, Player wins: The AI gets a point of BadCommander and the player gets a point in PlayerGoodCommander (ie. in effect half a point of GoodCommander). This is undesirable since the AI has gained an advantage over the player compared to an AI via AI battle.

Player vs AI autocalc, AI wins: The AI gets a point of GoodCommander and the player gets a point in PlayerBadCommander (ie. in effect half a point of BadCommander). This is undesirable since the player has gained an advantage over the AI compared to an AI via AI battle.

Player vs AI fought, Player wins: The AI gets two point of BadCommander and the player gets two point in PlayerGoodCommander (ie. in effect a point of GoodCommander). While the player result is as desired, the AI is suffering unfairly.

Player vs AI fought, AI wins: The AI gets two point of GoodCommander and the player gets two point in PlayerBadCommander (ie. in effect a point of BadCommander). While the player result is as desired, the AI is benefiting unfairly.

Note that I'm ignoring battle odds for this to simplify the tests.