Yes there is a prime timeline. I gotta hand it to JJ Abrams for throwing the biggest monkey wrench of all time into the Trekkie collective.
But what is the prime timeline anyway? There haven't been any Eugenics Wars that I'm aware of so Star Trek takes place in an alternate timeline anyway.
Didn't author Greg Cox handle the Eugenics Wars in his Rise and Fall of Khan Noonian Singh books in a way to reflect a Eugenics Wars taking place in the 90s, but under the radar of history, so to speak?