What is important to remember is that Trek is a fictional media franchise. The rules of time-travel work whatever way the writer decided it does. Star Trek has used both the "changes to a single timeline" & "changes create alternate timelines" depending completely upon what the writers have decided and what makes rational, logical sense to fans.
Disagree if you want, but I am of these opinions:
1. Time travel affects only the original timeline unless specifically stated by the writers through an episode or film.
2. Time travel issues band-aid themselves because, as stated by Spock in City on the Edge, "time is fluid, like a river, with currents, eddies, backwash." As long as it wasn't some major thing like a death that wasn't supposed to happen, the water doesn't look any different "downstream."
3. Enterprise naming conventions are just a normal (not thought up during previous series) continuity error (Enterprise was retired before the Federation formed and is thus not the "first starship to bear the name")
4. nuTrek takes place within a different continuity entirely. Nero & Spock-a-cola Classic didn't just move backwards through time, but sideways as well into the past of an alternate universe entirely. One where things looked different & smelled different already (explaining why Benedict Cumberbatch is now a white guy and Starbuck is female). Where the past has not yet been affected by people from the future.
4A. No one from a different, "possible" future changed this universe's past either. No Enterprise-A crew in 1980's San Francisco, Enterprise-E crew in 2063 Montana ,etc. This universe has unfolded as it did originally. So far*
*changes will eventually be written in by nuTrek's writers.