I'm trying to find some info

What do the “In Eternal Palace”, “In Ny’alotha” and “Fighting Aberrations” actually do? I can’t seem to find this information.

There are a couple items with effects that only work in specific situations and these options tell AMR to include those effects when optimizing.

Specifically that would be:
“In Eternal Palace”: Special bonuses of Benthic items from Nazjatar (see Wowhead’s guide)
“In Ny’alotha”: The set bonus from Ra-den’s trinkets (Titanic Empowerment)
“Fighting Aberrations”: Increased damage of the minor effect of the Purification Protocol essence

I’m not entirely sure if that’s all of it, but those are the ones I know of.