Aliens were behind the Chrysalis Project
Look, the author did a lot of research, but it's still a bit of a stretch to say human beings in the 70s had access to this level of genetic engineering technology. Also: 1) Dr. Kaur mentions some friends who were privy to happenings at Area 51, and 2) Gary Seven is strongly implied to have some kind of alien enemies in "Assignment Earth" and the documents originally pitching his series. The Augments were specially selected descendants of history's greatest criminals
Including Professor Moriarty, Fu Manchu, Captain Nemo, Dr. Mabuse- et cetera. The use of the word "eugenics" definitely suggests selected breeding rather than/in addition to genetic augmentation. Tying into the above WG, while the scientists heading Chrysalis seem utopian in their thinking (if insane), it would make sense if at least someone inside the operation fully intended to create a race of conquerors to destabilize world peace. So they set about breeding their own, from the perfect stock. Khan wrested control of Muroroa Atoll from Cobra
Lots of competition in the megalomaniacal lunatic business.