: Possible Thoth's cores are distributed across all of those locations, and in
: different timelines different teams of humans (not always including the
: player-character) activate different ones.
Also, in M2, Blake's humans had already been trying to activate Thoth for a while before they rescued the player, so it's possible that they might have hit a few sites already by that time.
However, I don't think the location in "Strange Aeons" is actually Thoth's core. Like Durandal, Thoth is software, and can transfer himself to other computers as needed, and Thoth is already active at the time you go to SA (presumably activated by Durandal's humans), as he has been sending messages to you on the previous level. The purpose of the facility that we power up in Strange Aeons seems to be for merging the two AIs, and Thoth presumably transfers themself to it once we power it up.
This also explains why (in-universe, anyway) we needed a new uplink chip in Strange Aeons—this ancient machine certainly would have a different interface than Durandal's ship. It'd be like trying to insert an SD card into a CompactFlash reader.
We could also just say the nitty-gritty details of map layouts are non-diagetic, I guess.
As for Durandal defeating the Western Arm on his own without the S'pht'Kr, 1) he explicitly says he can't do that in M2, and nothing we ever see in-game suggests otherwise, and 2) Durandal is an egomaniac, and it's completely in-character for him not to share credit—heck, he won in M2 via a Hail Mary pass and still is all like "He couldn't break me. No one can." in the ending. It's left open-ended, and the specifics aren't clearly stated, but my interpretation is that the player's first attempt was to have Durandal run a bee-line straight to Thoth's core, without spending all that time poking around, establishing a base, reading history terminals, exploring the citadel, etc., in the hopes of getting done and leaving before Tfear can fire the trih xeem. It's a logical first step, and probably the first thing a player would try to do on a replay, but it would involve skipping all the exploration that revealed lore about the W'rkncacnter, hence Durandal's lament at not having more time.
