It’s of note that of Kirk’s two appearances in SNW so far, they have both been alternate timelines versions

I noticed this too and really want this to be a recurring gag in the show. I want every appearance of Kirk in SNW to be an alternate timeline version or Section 31 double or android or candle ghost until the very last episode in the series, when the "real" Kirk turns up to take over the Enterprise from Pike.

I'm half-kidding but also half-not. Modern (by which I mean Kurtzman-era) Trek bringing back legacy character after legacy character in ostensibly new shows is the trope I'm least impressed by. So the least SNW could do with Kirk is subvert it in a fun way.

Sera’s explanation that this was “supposed to happen in 1992” and time itself is pushing back against attempts to change it, events reinserting themselves, now provides an explicit mechanism as to why the chronology of the Eugenics Wars has changed.

The real-world reason of course is that they wanted a scene where L'An meets young Khan but also wanted to set the episode today; likely to save money, but also because having characters travel back to the "here and now" instead of 30 years ago is more relatable for the audience. Which is why "Tomorrow is Yesterday" was set in 1969, The Voyage Home was set in 1984 and "Future's End" was set in 1994.

But the explanation offered in this episode also explains why the Eugenics Wars weren't evident in "Future's End".