I don’t feel like Pyr wrote E43. The person who wrote it feels like they don't know too much about the story, yet it seems like Pyr is very knowledgeable about it. Then again, it might be that Pyr is just acting like he knows everything and is trying to deceive the burned man for whatever reason. (Especially after what he said during reading Aloy's second entry, it makes it seem very possible that he also is experiencing the story with the burned man for the first time, or doesn't know the story in great detail.) They surely fooled me if this is the case.
It makes a lot of sense if the comment made in E45 was Pyr since that is how they are, but one of the problems I have with the idea is that it was not said in the backlogs. Pyr's jeer towards Neru and Shax during the prologue only happens in the backlogs yet this can be seen during the game. (If it’s possible that he can insert himself during the story like this, I find it strange that he doesn’t constantly do it more often. Unless someone is stopping Pyr from doing it, I don’t think they have the ability to do so.) The other problem I have with it is that it affects the actual events of the story. This is the continuation of the quote.
E45Con
This implies that Shax was feeling an effect during that moment, and Neru was able to pick it up with his smell. Unless Pyr has the ability to somehow change the events or overwrite what Shax was actually feeling during this time, I don’t think the comment in E45 was from Pyr.
Maybe you’re right with E47, I might be just looking a bit too hard on it, or too little on it. But I still can’t help but still find Bernardo switching from being indifferent to having a playful attitude to be other than suspicious. In all the sense of the word, I find Bernardo to be sus. 
Hopefully, it’s all in my imagination, and there is nothing to it other than what you said about it. I just don't want Bitey to get hurt anymore, nor anyone else in the story. (However, it seems like there is no other choice at the end.)