The lore books are written from an in-universe perspective and that of an outsider to boot. Beast of Winter gives us a chance to converse with the parties involved first hand and get a look at how it actually happened thanks to the Watcher gifts. It's not necessarily contradicting, you just have to realize that the stories told about events and the events themselves are not necessarily the same.
I mean, in a broader sense, the Pillars story is about identities and the factors that shape them. Engwithans imposed a new order, a new identity through their religion. This order lasted for a time, upheld by the Leaden Key and the structures of power that dominated them, but as humanity develops and wants to forge a new one, the gods struggle to reconcile humanity slowly learning to exist without them and their own centuries-old identity as divine beings essential to the world.
So Eothas wants to force the gods and mortals to reconsider and reevaluate their role in the grand scheme of things. He wants to give them the tools to build a new identity, but realizes that he is still clinging to the old notions of godhood and relationship with humanity, so he allows himself to be (apparently) killed, creating a new myth.
I'm kind of rambling here, I need to refine this thought.
I guess that is one interpretation, but you could easily just say that this is a clear retcon.