Certain options will cause weird behavior since the game is expecting certain settings which the trainer overrides, you'll crash if you enable some stuff in the first mission for example as certain scripts set your health and shield down to 1 and in the second mission the no-reload option can cause a turret early on to crash the game as it shoots out several thousand rockets in a constant stream, looked pretty funny though, caused severe slowdowns as well.
Later on in that mission some option related to the use of special abilities causes a mortar segment to become unstable as you can lock on as many targets as possible with no way of cancelling out, had a lot of little red laser lights targeting the entire area before it crashed.
In short the trainer works as expected and everything functions great but the options should be used carefully to avoid causing the game to bug out and possibly also crash during certain scripted sequences.
(I believe the readme for certain trainers for other games have similar things mentioned.)
This uses CEG as well so for all I know there could also be some triggers used since that protection allows such behavior, I wouldn't know though but that could also perhaps explain some of these results if the game actively goes weird when it detects that certain things are altered.
I am totally agree with you here, as I am floating on the same board as you are. I notice that unlimited ammo option cause the most game crash