As I said, though, that's exactly what the word "retcon" is supposed to mean -- a change that is perfectly consistent with what came before. It's short for retroactive continuity, not contradiction. A successful retcon is one that does maintain continuity, that fits in as if it had been the case all along. So yes, it is a retcon, in the original sense of the word.
I think that was exactly the idea in "Space Seed." In real life, the eugenics movement got started in the 1880s and there were a lot of genuine efforts to improve humanity through the kind of selective breeding applied to plants and animals. It was a prominent movement in the late 19th and early 20th centuries, though it was usually driven by white supremacism rather than good genetics. It was a major driver behind the Nazis' beliefs, which is why it fell out of favor after WWII. But I take "Space Seed" as positing that at least one eugenics program -- one that more intelligently embraced genetic diversity rather than whiteness -- continued in secret and eventually succeeded. If it had started in the mid-1880s and produced a new generation every 18-20 years, say, and if Khan was born in the 1960s, say, then he could've been a fifth-generation product of the program. Cutting it a little close, less than a century, but certainly more plausible than assuming it was all done in a single generation.
As I remember, there is a famous example of successful eugenics in science fiction - the Howard families in Heinline's future history. In 19th century San Francisco, wealthy Mr. Howard left his fortune to improve humanlongevity. His executors use slective breeding. They looked for young adults people who had four healthy living grandparents and offered them money if they would marry someon on the list of people with four heatlhy living grandparents. After a few generatins it produced people who lived for centuries.