The OG reason for the Eugenics wars was to give an apolitical reason for WW3. USA vs USSR was fully expected to go hot at some point and the idea was that the post-war period would cause a world wide reflection and unification.

First Contact messed with that by having rival groups still fighting a stagnate war at the time of the first warp test. Remove the works of Rick Berman and it becomes apparent Roddenberry wanted a cohesive timeline that culminated with the idea of global peace as a precursor to the Federation.

All that said: augments and eugenics were a really good reason to have a global war between superpowers. Khan Noonien Singh controlled a huge chunk of Earth before escaping into space. He was a stand in for a successful Hitleresque leader who used fascism to create "perfect people" that he could control.

Augments became shorthand in the future for Gestapo.

Again, all of this is without First Contact or DS9 setting the stage for the Bell Riots and the other WW3 that ended in 2053.

With all the edgy things directors want to do these days, making a pre-star trek eugenics wars movie with only small nods to the franchise might be a hit without stomping all over trek as a whole. (Nods like a Montana research facility with a blueprint in the background) All pre-warp.

At the end, have a line that says "Continued in Star Trek: First Contact"

Star Trek wasn’t just a show about social commentary, it was also about nerd stuff: science fiction jargon (technobabble and technical plot devices), world building, gratuitous displays of competent leadership working with competent implementers, having sex with aliens, and playing the trombone!

In other words, Star Trek is allowed to have stuff in its backstory that doesn’t comport with progressive messaging. I see Trek’s Eugenics Wars as a wonderful counterpoint to the Dune universe, which features pervasive eugenics and a dearth of computers. Dune’s anti-AI message may fit the zeitgeist like a glove right now, but that’s more due to luck than anything else. From the perspective of the 1960s, both AI and genetic engineering seemed equally remote (and tantalizingly close).