...Have the dates for the Eugenics wars been revised or are they still considered to have occurred in the 1990's. If so, then the Trek time line exists parallel to ours (slightly depressing)
I chalk it up to the writers of the episode creating a future past for the episode and not imagining we would be here 50 years later to discuss it in terms of canon. In other words, I dismiss it as a real world consideration of a fictional show trying to be futuristic 50 years ago, and getting it wrong in their crystal ball.
I consider TOS and all but the Abramsverse to be in our timeline or universe despite the mistakes made about the Eugenics Wars. I just ignore and dismiss it - like errata - and I feel fine. You can do the same if you choose. Conversely, however, I do feel distant and disconnected from anything in the Abramsverse because it isn't ours. It's a fundamental problem for me.