Problem is, that lore also restricts which Larian obviously was not a fan off. Thus they ignore past lore whenever they please.
If true this is sad to me. If the lore is to restrictive for an IP then use a different IP or create your own gaming world. Grabbing an IP and then ignoring the lore to me is a pure exploitive use of the IP and just lame.
Not much lore was done dirty imo.
The only things that spring to mind is the weak reference to the threat of the Cult of the Dragon (CotD) that Wyll claims to have made his pact to defeat. If you ran those adventures the CotD was at least as powerful as the Absolute. Imo, Mizora simply tricked him and/or he's an unreliable narrator.
Oh, another is Aasimar. Aylin might be a kind of Aasimar, but she is not the usual type.
[Edit] The heartlands terrain. It's not presented as raised sandstone scrubland, but verdant grassland (and Trielta crags are north-east). But this can be handwaved as local terrain and abstract maps. Besides, it's beautiful.