I feel like, to answer why the federation time-cops are letting this slide is because fundamentally, it doesn’t change much, the events still happen and affect the current galactic-chrono-political thing they have going on, and if they do interfere they could be facing an all-out time-war/“Temporal Hot War” with factions like the Sphere-Builders, Romulans, Na’Kuhl, The Mysterious Benefactor of the Suliban, and other factions that have not been revealed. So I’m willing to think that they are letting that slide so that the timeline isn’t damaged irreparably. And they do state that the Temporal Cold War and its factions are trying to eliminate Khan since he’s the focal point of the Federation’s creation (and kind of what separates our timeline from Star Trek’s), they’ve pushed back Khan 30 years. She does say that she arrived in 1992 and was waiting 30 years to kill him.

To answer your second question and side note, those events will still fit. Just because Khan was moved up doesn’t change the whole timeline. To be fair, in “Past Tense” and “Future’s End”, those cities don’t exactly look like they’ve been ravaged by war, so it’s more likely TNG, VOY, DS9, and SNW are their own timeline rather than TOS, TNG, VOY, and DS9. Plus, 49 years is more than enough time to have 2 wars in, especially if they happened back to back.

And, to be fair, Star Trek isn’t exactly a strict timeline. We see some differing events all over, probably because Star Trek likes to give things dates. This doesn’t necessarily mean it’s a new timeline, just that the events happened other than what is said. Temporal Events in Star Trek are supposed to be taken with a grain of salt.