There are lots of ways that the death toll in a war can be calculated. The conceit of Greg's books was that a lot of real-world events were secretly caused by the conflict among the Augments (although that term wasn't in use yet), so that a lot of deaths we thought of as having other causes were retroactively attributed to the EW.
Although as I've said before, the "secret war" angle of the EW books only makes sense from an American perspective; we're so insular in our awareness that we could plausibly overlook a massive global conflict, but there's no way the people of India and Southeast Asia could've been unaware that they were ruled by Khan Noonien Singh. And while the books do recontextualize real events as part of the EW, they don't really play up the secrecy angle all that intensely. So I think it's possible, with a little flexibility, to interpret the novels as depicting key parts of an alternate history that overlaps ours in a lot of ways but also entails a larger, more overt conflict.