It's not clear when the Eugenics War were. We have the late 20th century (TOS, TAS), the mid-21st century (ENT), or the mid-22nd century (DS9).
Well, it is called The Eugenics Wars
, so there's no reason why it couldn't have been a series of separate wars connected by a common theme, such as genetically engineered supermen and/or cloned, cybernetically enhanced, or disposable soldiers like the drug-addicted soldier from 2079 in Encounter at Farpoint
. That could explain why there was a war in the 1990s, why the war was confused with WWIII in the 2050s, and why Archer's grandfather was fighting in a Eugenics War in 2079.
I have issues with the USS Vengeance; namely, the issue of a covert black ops unit using this behemoth. The purpose of such an unit is stealth - you don't want to draw attention to your activities.
Space is vast. The ship could be ten miles long and still be "stealthy." Plus, Section 31 might be taking a more active and overt role in this universe, and will flex their muscle publicly from time to time.