What? Sometimes the timeline changes (City on the Edge of Forever, Yesterday's Enterprise, First Contact...), sometimes alternate timelines branch off (Kelvin movies, mirror universe episodes, Parallels...), sometimes history is practically unchangeable (Time's Arrow), sometimes the transporter can full on beam some one into their alternate timeline erasing their memories (Time for Yesterday)...
"In a Mirror, Darkly" refers to Prime as an "alternate reality", exactly as the Kelvin timeline does. There was an episode pitched but never made which would have shown the inception of the mirror universe, involving time travel and transporters. And of course "Parallels" explains it perfectly. In one universe, Nero appears in 2233 and wreaks havoc, but in another he does not.
I'm guessing you've never watched "Tomorrow is Yesterday", "Yesteryear", "Time Squared" or any of the other Trek episodes where time travel plays by entirely different rules?
They've been making it up as they go along for 55 years now and not once checking what their predecessors did.
As I said, I never saw "In a Mirror Darkly," but I understand now that it basically plays by the same rules as Trek 2009, which is that time travel causes branching timelines.
In NO OTHER instance of Star Trek does that happen. In those other instances where time travel occurs and timelines are derailed, it's all about characters "fixing" the ONLY existing timeline to restore the imperiled future of our characters. It's "Back to the Future" rules - someone messed up the timeline, our future is in danger, now we have to fix it.
That happens in "City on the Edge of Forever", "ST: First Contact", "Past Tense", "Trials and Tribble-ations", "Yesterday's Enterprise" and more.
The point is that the timeline has been "broken" by time travel and the stories involve our characters trying to fix it by various means to "set things right" and restore the prime/sole/only timeline.
That even happens in your "Tomorrow Is Yesterday" example, where the crew monkeys around so that their time incursion into the 20th Century never happens (and the air force officer doesn't remember it.)
Time Squared is not a relevant example. Neither is "Parallels", which doesn't involve time travel at all.
Only in Trek 2009 (and Mirror, Darkly, apparently), do the characters say, "Well, we're in an alt timeline now and there's no 'fixing' anything, so we just have to live with it."
In Every. Other. Instance. The characters work to fix the broken past to save the future and get time "back on track." Because there's just the one timeline and the changes in the past have imperiled our characters' own future.