Spock's comment that Khan's goals included "the extermination of anyone not considered superior" (or words to that effect) sounded to me like it could be a reference to Khan's last-ditch plan to use his mother's modified strep-A to eradicate all non-augmented humans on Earth in Eugenics Wars, volume 2. That said, the rest can't fit.
I read the EW books in the run-up to ID, and I'm afraid I wasn't a fan of them. Although enjoyable in parts, they were too slavish to "Space Seed" in making Khan a Sikh, which was obviously a mistake by Marla. Sikh's are forbidden from removing hair from any part of the body, and Khan was not only clean shaven, but had a waxed chest too! I found the rest too fanwanky. A nice try to reconcile RL with Trek, but one doomed to failure. The framing story was a rehash of "The Masterpiece Society" and didn't engage me one bit.
Khan's racial identity is a complete muddle in canon, going from brownfaced faux-Indian in SS to White Hispanic in WoK to White British in ID. Now I'm thinking that he was never Indian; that was another epic fail from Marla (the pic of Khan in a turban was painted by Marla too, excusing that). He was only tanned - and he lost his tan on Ceti Alpha V in Prime Trek and in the Section 31 R&D labs in the AU. Thusly, all that's changed is his accent - no more of a big deal than Kirk's eye colour, IMO.
Admittedly this doesn't explain the complete change of his followers between SS and WoK. One thing at a time