I love this story (I think that Shin and the rest have come up with something that Hasbro should give them the license to if you ask me) and its a shame I don't have enough time to write as I used to. But I do have time to read and time to think about it. And one thing that really stands out to me: I think that Sunset is attracted to Pinkie but won't ever admit it or at least not anytime soon. This is my thoughts.
1) She's been through a bad breakup. Bad breakups are BAD. I suspect that she wouldn't want to do anything with Pinkie until she was absolutely sure that they're mature enough to handle such a relationship
2) Shin has been dropping hints that the two are destined to be together. In Book 5, Pinkie she tells Sunset that she knows where she belongs, and Sunset admits that she knows what Pinkie is and that it comforts and makes her afraid at the same time. The only thing that could do that would be a future wife
3) I suspect the magical ball inside of Pinkie is NOT the Sunset/Pinkie couple from that sidestory, but a future view into Sunset and Pinkie's life. The fact that Meena and Sunset of the other universe look older and have different hairstyles would have been noted by Pinkie. The fact that they didn't hints this is a view of the future and not the past
4) Jewel, or Fujistu or even Rose isn't the threat to Pinkie and Sunset. Jewel is an afterthought. Fuijtsu is a rapist that Sunset hates. And Rose seems to me to be wavering between choosing Sunset or going back to her boyfriend.
5) Something that Sunset said in Book 5 also bears out. Faust likes happy families and happy endings. What better way to give her granddaughter someone who will always be there for her then to give her the one girl that is so deeply in love with her that she probably considers herself tied already. Pinkie doesn't act like a girlfriend, yandere jokes aside. Pinkie acts a lot like a newlywed wife towards Sunset and I think this is a clue that they will be together in the end.
6) From what I can tell Shin likes to hide a lot of stuff in his stories and you really have to think about it. I found a huge thing which I think is a clue. It was my girlfriend (who also reads the stories!) who pointed it out: from the moment that Pinkie confesses her relationship to Sunset, there are a lot of erefences to magenta from that point on in Shin's stories (and might also be in Blue's and Flint's stories too). While meganta is a darker shade of pink and probably the color of Pinkie's hair, it's also worth noting that magenta is a shade of pink that's made by mixing red, yellow and pink together. Sound familiar?
Those are just my thoughts on it. Personally, I think they make for a perfect couple and it will be interesting to see where they end up.

6867531
Regarding point 3) I will say that the magic ball universe inside Pinkie can only be an alternate reality for the simple fact that Mina and Sunset's past is completely different from what happened in 7DSJ. For one, Sunset was never an alicorn and has lost the ability to do magic at all. She was also never adopted by Twilight's family, as Twilight herself became essentially a magical school shooter egged on by the sirens, who were more in line with their canon selves rather than paramilitary child soldiers from Canada.

Secondly, according to Shin our color expert, magenta is actually what you get by mixing red and blue. Red, yellow and pink when mixed produces tangelo, a shade I don't believe has been mentioned.

Some well-reasoned theories otherwise. Naturally, there's still elements in play here that you don't know about yet, and on that note I'm quite surprised that people seem to have forgotten all about Pinkie's visions of the Megan from 7DSJ: Downtempo, and the things she told her....

6867897
To add to Flynt's point, if the reality sphere in Pinkie was not an alternate universe and instead a glimpse into the future, it woudln't be a reality sphere, but instead a wormhole, and Sunset, regardless of her feelings for Pinkie or not, would not let something like that exist within Pinkie, for mere reasons of causality. Meeting an alternate version of you (as we have seen) is fine. Meeting your literal self at a different part of the timeline? Could be very problematic.