Autumn's reasons for fighting the player despite betraying Eden make perfect sense: he wants to rule the wasteland with an iron fist but has the human sensibility and basic decency to understand why poisoning basically the entire non-Enclave population is insanity.

The real idiocy surrounding the main conflict and ending is why the "evil" option available to the player consists of following Eden's plan, for which there is no feasible reason other than deliberately playing the most evil route possible for its own sake, rather than joining Autumn.

As an aside, Autumn is still one of the absolute worst "final bosses", if you can even call him one, that I've ever seen. New Vegas pulled off a confrontation with a non-superhuman enemy commander much better with General Oliver's fight.

Fallout 4: DuH wE nEeD bIg EnEmY tO sHoOt. Oh Me KnOwS lEt'S bRiNg BaCk SuPaH mUtAtS aNd MaKe ThEm AlL dUmB cAnIbAlS.