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From what I saw while messing with the data, you only get one dream in the second sequence each time. It's weird, but I don't think I remember any of the sequences from my previous playthrough, but that might be due to the story just being so intriguing. The first dream sequence is always the same if I remember correctly.

The one that implies Noch/other archons are listening in is the "fifth" one, in which the meta-character thinks that they recognized some characters in the dream, leading me to believe that it's actually not Nerus due to issues that Nerus never met Noch. (Coincidentally, the three with the "plan" to open the portal were the only three that new Noch existed, so it also plays well into that theory.)

The traitor being the meta-character is something I'm somewhat in support of, as I didn't find any evidence against it. It just seems... strange that Noch might be it, regarding Noch's position of power as an archon; how would anyone manage to manipulate them to such a degree?
Going out on a limb, my theory on who among those three would be Aloys, due to the comment about the "black fur on my skin" when first regarding their condition. Aloys is the only one among those three who ever had skin, or fur. Obli had scales and feathers, and Noch had a membrane, but Aloys became a werewolf through training, after being a human, resulting in their experiencing both skin and fur. But the comment about burned skin being unusual also strikes me as a bit odd. I'm left to wonder if the meta-character is actually in their original body or not.

I don't think that the meta-character removed their own memory. I used to be an avid reader of SCP (which led to a minor shock when I saw the Time Egg backgrounds had the word 'scp' in their file names, and I still don't know how to interpret that information), and whenever there was a breach in information in Series 1 incident files the Foundation would almost always use amnestics to force people to forget what happened. There are also anomalies that can make you forget certain things, and it's not out of the question that their entire memory was wiped through the power of someone/something else. I doubt that it was actually Pyr who made them forget, since they seem to mostly be jeering the lack of memory rather than exploiting it.
If the theory about Pyr having some sort of time-travel ability through the use of the Time Egg is true, though, then it might actually be Pyr exploiting the meta-character's lack of memory in order to interact with the past in some way. The Time Egg is still the pause screen for the Prologue, implying that we did watch that as the meta-character, but with a confused sense of self, or a level of immersion that surpassed that of Chapter 1, due to an only-partial torpor.

This also brings back into focus the facility -- how many people are in it? One facility for one traitor seems somewhat excessive, and what exactly is it that was chasing the meta-character was running from in Chapter 1?
Also, why did the Prologue use first-person pronouns instead of third-person like Chapters 1 and 2, despite Pyr's ability to interject, and again, what are the nature of those interjections?

A final tip, this one on datamining -- it's somewhat similar to installing Minecraft mods, if you've ever done that manually. Just click on what seems like it might be right after starting from the same place, and you'll find your way there eventually. The files you want have the extension .rpy. 
Happy mining!