exactly same issue, i've posted about this on the steam forums.
I just completed a new playthrough picking alchemists while going down Emrys' route again. Picked easy this time since I wanted to test out the no stealing route. I had a few new scenes with Illyria due to the Alchemy branch but still received the same bad ending.
I again maxed out war effort and Emyrs' romance, kept my wood and darkness at or above 200, made all the factions have over 50 approval, and like previous play throughs I was at 0 suspicion.
I'm genuinely at a stump as to what I need to do.
edit: I've also made several different choices in the story, such as the peace or fight option when asking about certain blonde sibling.