There's also the fact that the 24th-century shows often referenced World War III as a conflict that culminated around mid-century but never referenced the Eugenics Wars. If the EW were a global nuclear exchange in the 1990s, then surely the conflict that ended a decade before First Contact would've been called World War IV instead. So if IDW has indeed chosen to depict the Eugenics Wars that way, it's an extremely strange choice.
Yes, it does seem strange but this could also be a 'Usual Suspects' moment. Just because we have knowledge to contradict Khan doesn't mean the characters do I suppose.
Or of course proof that (IDW) Nero did not come from the Prime Universe.