Also I know this is splitting hairs, but "Space Seed" doesn't even actually say "genetic engineering", Spock refers to Khan and Co. as having been "selectively breed". It's not until Wrath of Khan when they get into the "artificial" genetic augmentation stuff.

That’s because genetic engineering wasn’t a thing until the early 1970s. When Spock was talking about eugenics, at that point in history it was purely a case of not allowing certain people to breed and making sure that only the “right” people were matched for the “best” offspring. That’s right out of the Nazi eugenics playbook, so despite the South Asian aspect of Khan’s supermen the expectation that they would become fascist and tyrannical was never in doubt. So Khan would never have been NOT a khan, and “Space Seed” does a good job in portraying the insidiousness of the eugenics argument and the seductiveness of it, what with McGivers being turned and even the senior staff expressing admiration for Khan, describing him as the “best of tyrants”, to Spock’s horror. It’s played off as a joke, but it does show how easy it is to buy into the “better world” rhetoric.

I would love to see an episode about a species who's had their own Eugenics wars, or perhaps even one who's embraced gene augmentation, or goes full-on "Khan did nothing wrong".

We’ve got TNG: “The Masterpiece Society” right there, which is a ready made premise for a sequel. Maybe after Picard made off with a sizeable chunk of their population, throwing it into imbalance, they resorted to more desperate means. And desperation does breed darker motivations.