They might yet get changed later, considering that requires new voiced lines, while changing item descriptions is easier. Otherwise I'm not sure why Larian would bother to rewrite item descriptions.
Anyways, now I suspect the main plot is connected to hells, souls and the resurrection business, and the mind flayers are just being used as tools. Apart from the books in the chapel , in the fake doctor's basement there is a "nobleman's portrait" lying on the floor, which depicts Mizora (funny enough if you pick it up, in the inventory it will show a nobleman ). And that wizard was doing experiments on raising dead.
There is also a letter in the harpy nest written by a warlock who, from the description, sounds like he was working for Raphael. There is a crashed boat next to the nest, so perhaps they were lured by the harpies and crashed. What is interesting is the old journal lying next to the letter, though it could be simply an easter egg. Or the warlock was carrying that journal.
). And that wizard was doing experiments on raising dead. 
