I'll do RRR as soon as I can, but I have to play it first! Don't fret, I caught up by finishing M2 (in gameplay), I won't take too long.
This write up has no pretense that readers may not have played infinity yet, but even with the spoilers of foreknowledge we're still rife with confusion. As for TFear's omission of the S'pht'Kr outbreak in his transmission, I think he figured that the unknown chaotic force will do them in anyway, so he may as well inform the high command that he is dying a heroic death at the hands of an incomprehensible force than admit the embarrassment that western arm was forced to use Trih Xeem because they can't beat some lost s'pht clan and a rampant AI. Durandal realizes his defeat because he now knows the w'rkncacncter is real, hence his warning.
I have a theory that M2 is on a separate timeline from M1, and the timeline we're about to enter is what logically follows after the end of M1. In Ingue Ferroque, Durandal and Boomer already left the system without you and said his goodbyes, so how could he have teleported you into stasis on the boomer after that? Being captured by Tycho in the 2nd sacking of Tau Ceti makes a lot more sense. I even have a theory that Durandal took one of the other cyborgs and implanted it with your memories, so the player in M2 is a different cyborg that thinks it's the cyborg from M1. Tycho said the deaths of the cyborgs were indistinguishable from the humans on his sensors, so how does he know all the cyborgs were even there?