Pike and Spock (who himself was kidnapped and augmented by an Illyrian governor), found out that the Illyrians weren't always augmenters (the kidnappers didn't know this either). The Vulcans actually experimented on them first on their original home world (which is now inhabitable), which caused them to continue it for survival. As time went on, that knowledge disappeared. So the only history known to everyone, including the Federation, is that they've always augmented their bodies on their own. Pike, Spock, and the Illyrians agreed to not reveal this to the Federation to keep the peace and preserve Illyrian history. Damn Vulcans.