I hear ya, I didn't understand it either. I talked a few things out here, but still was confused by it. After a few weeks, I took another shot at it and it was much clearer with the "flash backs' being more obvious to me, easier to follow.
I would say TFS confused me about the ending of TUC more than anything - I was expecting some serious shit to go down with them, but either they were all dead by then or were routinely dispatched of - which is not a criticism, I LOVED the ending, just trying to figure out what Bakker had in mind with TFS.
You know - Bakker has mentioned a few times with his Q&A sessions with us that it appears we missed something regarding The Consult ( one example was someone questions validity of The Consult bringing back Dunyain, Bakker said ( paraphrasing ) we missed something to ask that question and left it as Humility wasn't a feature of The Consult psychology ). Hmm ... making me think that maybe they "need" to be led, part of their genetic engineered pathology. We see Aurang "teaming" with Shae in a way suggesting more than simply strategy, collecting/corrupting allies for their cause. And we see Aurax cower before The Mutilated when he hears of his brother's demise. Maybe they're are all part of "machinery" ... more than techne enhanced, but purely techne generated - though they are damned, so maybe not. I don't know, it's like I'm on to "it", but keeps escaping me and I find conflicting evidence to any conclusion I attempt to draw.