E43
That's a fairly interesting observation, I must admit.
Hehe, you finally found the key for Pyre's messages in the prologue. Although, it's not the only time that he injects his thoughts -- the one scene near the end of the prologue really set (them?) up as an enigmatic character, and is part of the curiosity they hold for me. They seemed to be trying to be disruptive.
E44
Nerus is one of the Great Shapeshifters, and given that I don't think he necessarily had problems with his parents -- otherwise Nomino has executed a massive deception (not like he hasn't done it before) about the nature of the Great Shapeshifters. I do think that it might be reading a little bit too deep, but I don't think it's impossible you're onto something there.
E45
I'm a bit surprised you haven't picked up on the entirety of Pyre's dialogue surrounding the Prologue -- he's trying to mock Nerus for not having noticed Shax's illness here. I'm 85% sure that's what it is, otherwise a lot of Pyre's dialogue might lose its meaning.
E46
I didn't think about the possibility of the descendants using one of the Aeon Wars to cripple humanity before, that's a pretty interesting theory.
E47
If you were re-reading this, I think that the second quote you posted was actually foreshadowing towards the fact that Bernardo and Bitey end up in a relationship as we see in Chapter 2. There's plenty of information dropped beforehand to indicate that Bitey is interested in men, and as a person who has been spending more time with non-heterosexual people I can say that it definitely strengthens your ability to pick up on others who might be interested.