Originally Posted by Zloth
From what I can gather, the aliens have a small patrol route they follow. If a soldier moves into sight range of an alien group then they do the little cutscene showing them hissing/beating chests/whatever and move off to cover. If the aliens move into sight range of a soldier on their turn then you see them appear off in the black, they move to their appointed patrol waypoint, do their little cutscene dance, then rush off into cover.
As far as I know, it's the same with or without the mod. (Except with the mod you'll often only see three aliens in the cutscene when there are actually four or more.)