The biggest one that stands out to me is a change from either Patch 7 or 8 - the Thralls on the Nautiloid now wear the cult and symbols of the Absolute.
that's interesting, I never looked so closely at what they are wearing.
I always interpreted the fact that you are attacked by the 'siblings' when you tell them you came from the ship, that they dont actually realize that the cult has anything to do with mindflayers. Priestess Gut doesn't either, and neither do Ragzlin and Minthara.
