Timeline has been changed multiple times by multiple series. Timeline still seems corrects itself. Strange New Worlds is just following what was previously established most recently. That World War 3/The Eugenics war was in the early 21st century, as established in TNG and further cemented in place by both First Contact and Enterprise.
I do wonder if we've seen such a huge change in the timeline as "Tomorrow, Tomorrow and Tomorrow" represents before?
It is clear that Khan simply can't be the same character here that we saw in "Space Seed". There's about 70- or 80-year difference in his birth between the two episodes. Tough to see how the timeline can play out the same with someone who is going to be a different person. That and a war that is happening about 70 years later than was originally intended.