: Huh, that's a connection I'd never made before. I've sometimes wondered if,
: instead of actually occurring in separate timelines, we're just repeatedly
: altering the same timeline via plain old Back to the Future-style time
: travel, rather than actually jumping between discrete timelines.
It's very clear that you are exploring different timelines or alternate realities. There are mutually exclusive events that take place, as well as physical reality being different: Aye Mak Sicur station is presented in two different forms, and the physical location of Thoth's cores is different in M2, Despair, and Envy.
: Durandal hasn't sent
: the player to explore L'howon, although he has apparently slaughtered
: the Western Arm, suggesting that he somehow managed to call K'lia,
: possibly by jumping straight to having his humans activate Thoth and
: skipping all the early fact-finding stuff from M2. Regardless, it didn't
: work, and the player finds himself starting back.
The implication is that Durandal hasn't explored Lh'owon at all, with the main character nor in any other fashion. He just defeats Battle Group Seven on his own, as he states: "I slaughtered the Pfhor naval garrison and the Western Arm of their Battle Group Seven". If the S'pht'kr were summoned, this would definitely been mentioned by him. His ability to defeat the Pfhor on his own is simply an arbitrary difference in this timeline, possibly due to him setting up a trap for the Pfhor rather than exploring Lh'owon.