Set = One of Satan's chief 7 son.
Evil or Darkness = Underworld.
It's more of an alchemical role perhaps playing with words and whatnot. It seems more like representations of Yin(Shakti) and also representations of Nigrido stage alchemy.
Remember the Gods play roles to express mental, physical, spiritual, allegorical, and also alchemical aspects. Unfortunately humans have a very black and white understanding and believe what your saying "Set is evil". Eh...it's similar to Sanskrit stories Gods playing roles of adversaries or whatnot to express an understanding. It's simply the Gods roleplaying to make people understanding.
Unfortunately when humanity rebuilt itself 10,000 years ago from the enemy attacks. They were already rebuilding based on corruption, degeneration, and limitations of attainment of spiritual truths and advancement. Hence why civilizations began to collapse and focus on the material aspects like literal stuff.