Are you saying the universe that Spock Prime is from is an alternate Universe? What are you basing that on? It's not like we've seen every Federation or Romulan ship ever built. . .
I view the universe that Spock Prime came from as not the original Trek universe in terms of some aspects, such as the visual style. So for example, the events of TOS more or less took place, except the Enterprise looked like the "Abramsprise". I'm not tying to force this opinion on anyone, it just works better for me to look at it this way.
I have to admit though that I do kind of go back and forth between the reboot and alternate time line arguments. I can't seem to pick a side.