ENTERPRISE took place in the main Trek universe, since Borg from the 24th century were found on Earth in an Enterprise episode...the crash having taken place in the Picard movie First Contact.
Unless you consider that the Borg, then Picard, each created a new alternate timeline, and Picard returned to the future of this third "Enterprise" timeline at the end of that movie, which was "close enough" to the one he remembered.
"Star Trek XI" simply starts 200 years later in that new "First Contact"/"Enterprise" timeline.
There was never anything said about the Enterprise crossing into a parallel universe in FC. Rather, considering the fact that THEIR Earth was changed when the Borg changed history, Enterprise E went back to the past of their own reality...the mainstream Trek universe.
You are making the mistake of assuming there is only one "mainstream" universe. TNG's "Parallels" established that there are numerous parallel timelines, each of them equally real. What you subjectively call "mainstream" is merely the alternate timeline where the TV cameras happen to be recording on a given week.
"Star Trek: First Contact" depicted the same treatment of time travel as "The City on the Edge of Forever" -- when McCoy/the Borg go back in time and change the past, the captain (Kirk/Picard) is pulled into the future of that new timeline where the Federation no longer exists. He then decides to go back in time and "fix" the past, then return to the present to find the Federation exists again.
While those two episodes are consistent with one another, other episodes, such as "Voyager's" "Endgame" and TNG's "Yesterday's Enterprise" show characters from the future going back in time, changing history, then staying in that new timeline, which is never "fixed" by anyone. That is exactly what happens in "Star Trek XI." The time traveler leaves the "mainstream" timeline forever and continues to live in a new, alternate timeline.
You are assuming that when Lt. Yar and the Enterprise-C went through the time rift at the end of "Yesterday's Enterprise," that the entire universe disappeared. But it was just the camera shot changing from one timeline to the other, since Yar was the viewpoint character for that story. As far as we know, the original timeline kept going without Yar. Picard and the Enterprise-D could still be fighting the Klingon war without her.
In STAR TREK, changing the past has never meant creating an offshoot reality. It changes the one reality of that universe, and can even be fixed by further time travel.
That is the case in a couple episodes, but is not a universal rule in "Trek." Many episodes have depicted parallel universes, alternate realities, and divergent timelines. In many episodes, such as "
E2," the characters themselves are wondering whether time travel creates a new timeline or erases their own future. In fact, in each time travel story, the characters are never sure what is going to happen, since time travel seems to follow different rules each time they encounter it.
In the "Enterprise" episode "In a Mirror, Darkly," it showed an interphasic rift creating a link between the TOS timeline to 100 years in the past in the "Mirror Universe," which would also have links with TOS and DS9 timelines in the "present," so there is precedent for an instance of time travel to also cross over into alternate realities.
Star Trek has been going for 43 years in the real world. Stuff changes. Until a few years ago, there were 9 planets in our Solar system. We now know there are 8. Star Trek is full of references to "9" planets.
Will all future episodes and movies of Star Trek refer to 9 planets?
Well, astronomers seem to change the definition of "planet" arbitrarily, to make themselves seem relevant. But I will stick with
the dictionary definition of a planet. Astronomers do not have the authority to change the meanings of words. When astronomers debate the definition of "planet," it is as pointless as Trekkies debating theories of time travel.
Stuff changes in the real world. You have to allow for that. Scientists used to think that changing the past altered the future. We now think otherwise, or at the least we think both theories are possible.
All time travel theories are equally fictional, just like quantum physics and wormholes and lots of other stuff that looks cool on a blackboard, but does not actually exist in real life. And "Star Trek" episodes certainly aren't written by scientists. That's why there are so many contradictions. There's no official rule book that governs the laws of Trek physics.
As I can't stand the original Star Trek series, this new movie which I LOVE has replaced it all for me. Now everything makes sense...
Enterprise > Star Trek (2009) > The Next Generation > Deeps Space Nine > Voyager
Actually, in terms of causality, the proper sequence should be:
TNG > DS9 > ST: First Contact > Enterprise > Voyager > ST: Nemesis > "Star Trek" (2009)