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.
Well the comic doesn't actually say the nuclear conflict was global, just that it occurred in the Americas, specifically the north continent. So while that might solve the problem of why it isn't regarded as being WW3 proper, it does mean that it would have probably taken the USA decades to recover from the devastation, so likely no LA as shown in "Future's End", no Millennium Gate in "11:59", and no Carpenter Street in "Carpenter Street." I can't see the nation being able to wage the War on Terror and the invasion of Iraq nearly a decade later either.