Meh, he does a brilliant job shoving them into the nineties. The TOS description of them, as an actual war and not a "secret" one, was always terribly evocative and made me think about the epic nature of a conflict where people who are indisputably Better Than Us have conquered the world, and mankind has banded together to fight them off and drive them back. In that regard, the books are quite lacking because the Augments never conquer, they just puppeteer behind the scenes.
Honestly, you don’t really need to move them to still have Eugenic supermen fighting humans for the planet. They could still exist in the 21st century, even with a 1992-1996 war.
It just wouldn’t be Khan. They would have to create new engaging characters.