There were many changes in STXI that contradict what Trekkers "know" as "fact". Most can be explained as being a result of the Narada's temporal incursion. But many cannot. Those that cannot precede the ship's arrival into the past.
The only explanation for that is that there was something else that had gone further into the past to make those changes, creating an alternate reality diverging at that point. And the Narada and the Jellyfish/Red Matter ship went to that reality/dimension/time period.
How?
Spock. He's the common denominator.
Spock has done numerous time jumps. But his last one in STIV just after his resurrection where he was using imprecise Klingon equipment and making his best guess, most would say it was different from his other jumps. (Just for the floating heads of smoke alone)
My theory is the point where Spock made his time jump into the past in STIV is the point in which the reality that STXI started in diverged from the Prime reality. And he became "metadimensionally" linked to it. The reality where Dr. Gillian Taylor went missing in 1986. So she never married in 1988, and never had the child she was supposed to have had in 1989. And 1990. And 1992. They never did check what her predestiny was to have been before their jump to 1986 (as they had done in their previous time travels), nor did they note any changes upon their return with the whales after all. So the cumulative reaction over time of her not marrying and having children could result in the changes we see in STXI a couple of hundred years later.
So when the super-nova combined with the red matter singularity reaction, all that energy created a portal that followed the link Spock had to this alternate reality his previous time jump had created. And being a portal, it's end dimension was set even though the time was not. It first opened way in the past and was making it's way back to the "present" at a rate of years for each second. Only becoming visible when an object goes through it from the Prime side.
So, that's my attempt to explain by connecting dots and filling in the blanks for an explanation I can buy. What say you?
ETA: Which also means that the portal is still there in the STXI alternate reality. And on that side it is going to remain, likely until the same point in time the portal was created in the Prime reality. While on the Prime side, it will likely remain open for seconds, minutes at the most, before the energy that created it dissipates. If there were any other ships or objects close enough to the Prime side of the portal to get to it before the energy dissipates, they could also show up in the reality of STXI. But nothing really can go back the other way (other than Spock Prime making another "time jump" I'd say). At best, it would pop up in the middle of a black hole a few seconds after Spock and the Narada had gone through. And good luck with that as it gets crushed and compressed down smaller than a point.
It could attract the attention of a Q I suppose. Or the wormhole prophets. "What is this anomaly? Send in the Sisko!" Maybe even the USS Titan (Riker was supposed to be working near the Romulans, wasn't he?). Hmmm... Captain Kirk meets Captain Riker... Any number of things are possible to further introduce into this new reality.
The only explanation for that is that there was something else that had gone further into the past to make those changes, creating an alternate reality diverging at that point. And the Narada and the Jellyfish/Red Matter ship went to that reality/dimension/time period.
How?
Spock. He's the common denominator.
Spock has done numerous time jumps. But his last one in STIV just after his resurrection where he was using imprecise Klingon equipment and making his best guess, most would say it was different from his other jumps. (Just for the floating heads of smoke alone)
My theory is the point where Spock made his time jump into the past in STIV is the point in which the reality that STXI started in diverged from the Prime reality. And he became "metadimensionally" linked to it. The reality where Dr. Gillian Taylor went missing in 1986. So she never married in 1988, and never had the child she was supposed to have had in 1989. And 1990. And 1992. They never did check what her predestiny was to have been before their jump to 1986 (as they had done in their previous time travels), nor did they note any changes upon their return with the whales after all. So the cumulative reaction over time of her not marrying and having children could result in the changes we see in STXI a couple of hundred years later.
So when the super-nova combined with the red matter singularity reaction, all that energy created a portal that followed the link Spock had to this alternate reality his previous time jump had created. And being a portal, it's end dimension was set even though the time was not. It first opened way in the past and was making it's way back to the "present" at a rate of years for each second. Only becoming visible when an object goes through it from the Prime side.
So, that's my attempt to explain by connecting dots and filling in the blanks for an explanation I can buy. What say you?
ETA: Which also means that the portal is still there in the STXI alternate reality. And on that side it is going to remain, likely until the same point in time the portal was created in the Prime reality. While on the Prime side, it will likely remain open for seconds, minutes at the most, before the energy that created it dissipates. If there were any other ships or objects close enough to the Prime side of the portal to get to it before the energy dissipates, they could also show up in the reality of STXI. But nothing really can go back the other way (other than Spock Prime making another "time jump" I'd say). At best, it would pop up in the middle of a black hole a few seconds after Spock and the Narada had gone through. And good luck with that as it gets crushed and compressed down smaller than a point.
It could attract the attention of a Q I suppose. Or the wormhole prophets. "What is this anomaly? Send in the Sisko!" Maybe even the USS Titan (Riker was supposed to be working near the Romulans, wasn't he?). Hmmm... Captain Kirk meets Captain Riker... Any number of things are possible to further introduce into this new reality.
I think my head just exploded with overthinking. 
