Personally, I wonder if Augment technology is derived from some of the first bits Starling sold off from the Aeon. Particularly in a post-"Super blood" Trek continuity
Even if the Aeon is part of the main timeline, the timing doesn't work. It would've probably taken many years to decipher any such technology and develop it to the point where it could be used to create Augments, and the interval between the timeship crash and Khan's likely birthdate seems too short. Besides, why would a Temporal Integrity Commission patrol ship be equipped with genetic engineering technology? Engines, computers, sensors, weapons, power systems, that I could buy, but biotech? That's a bit random, isn't it?
(Although, as I believe you're aware, I hinted in DTI: Watching the Clock that the Augment program was influenced by temporal intervention by Future Guy, doing the same sort of thing he did with the genetically enhanced Suliban, albeit more clandestinely.)