Hum. I just do not understand the "ideological grudge" comment if it's not at least the case that Alice thinks the blink performed a segregation of the two pre-blink factions.
Again, I do consider her judgment unreliable, so what she does or doesn't think may not reflect what's actually going on.
My working theory is that the blink segregated the biological faction onto earth and the tech faction into space, while rolling them both back to an earlier period in their history, where they could live in a way that more or less satisfied their prejudices, but kept them technologically crippled enough that the architects could easily control things. (Consider that Gavia's nano-tech didn't even come close to making her a match for Alice. Now, maybe Gavia is just some random girl to Alice's super-solider, but I'm betting that those in orbit, advanced as they are, are still a long ways off from peak human technology.)
In the intervening 5,000 years, the old ideological identities have faded, and someone is at least exploring the idea of a re-integration.
I agree with BenRG that the architects were powerful AI acting independently. And I'm sticking to my prediction that the Nightwalker(s) are a high level observer/control mechanism.
One more thing.
Alice: Do you ever wonder why, with all of your marvelous technology, there are no truly sentient machines?
Gavia: It's just not possible. The Praeses think, but not like we do, and they're not really machines either.
I read this as the Praeses having their origins in synthetic tech.
1.) Consider what Alice is asking in that first line. According to Alice,
only one faction had "truly sentient artificial life". It is (to me) heavily implied that the biotech faction emphasized "advancement of the [human] species by enhancement through biological means", as opposed to developing entirely new and powerful forms of biological life.
2.) So, when Alice asks why there are not "truly sentient machines", she's not asking why there are no instances of peak tech from either faction - she's specifically asking about the AI faction. In that case, if the Praeses were biological in origin, it would seem strange to me to make such a trivially obvious comment as "they're not really machines". For example, if the conversation is about instances of strong AI, I'm not going to bother to make a point to disqualify myself - it's trivially obvious that I'm not eligible to be an example, by virtue of being biological.
I think that, while the Praeses were given a physical form that is apparently reminiscent of organic life, they have (or, at least, once had) more in common with synthetics than biologicals.