I never really got the argument against augments (in universe as well as from the writers).
All the humanoids in Star Trek are the result of genetic augmentation anyway.
The whole “eugenic wars” thing always felt like a cop-out because the writers were to afraid to tackle a controversial topic during the actual show and pushed it into the past in a “we already had this discussion” kind of way.
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.
I only caught parts of ds9 - so sorry if this is obvious
but what? the other ww3?
Not to mention that in the 60s genetic modification was still in its infancy and a good sci-fi boogyman. Remember, Dolly the sheep wasn’t cloned until 1996.