Hello guys, this is the author. I realized that maybe some people wouldn't understand the ending of the story, so I thought I'd clear things up for you all
So in Tsubasa, one thing I noticed that was a recurring theme was the fact that two souls that are destined to be together are always together. Anytime they met a couple in one world, that same couple would be in another world. It's like, no matter what, these two souls will always find each other.
The beginning of the epilogue, if you didn't notice, was actually the beginning of Tsubasa (with a few alterations, I think), with Kurogane being sent to Yuuko's shop and meeting Syaoran (aka, the kid holding onto the girl for his dear life) and Fai, and then they begin travelling together. So it's like, because Kurogane and Fai are soul mates, they were destined to find each other again, somehow. And I thought it would be an interesting idea to make this inevitable meeting within the Tsubasa story.
And about the ending of the epilogue, my personal belief with the whole KuroFai thing is that Kurogane realized that he loved (or at least deeply cared) for Fai in Tokyo (aka, the world that was pouring acid rain). I think this because Kurogane's whole thing was that, after his parents were killed, he vowed to protect everyone he cared for and to never let his loved ones die again, and up until Tokyo, he seemed to not care about Fai. But when Fai was about to die from losing his eye, Kurogane did everything he could to save Fai's life. I also tried to make it like the beginning of the story. If you remember back to the beginning, the first chapter ended with something along the lines of, "in fact, Kurogane was sure that he hated Fai." And we all know how that turned out in the end.
I hope that makes sense... Long story short, Fai and Kurogane were destined to be together, no matter what world or time they are in, so the whole story was showing their destined lives together from another world, or maybe another time, and then the epilogue shows that their meeting within the Tsubasa universe was also destiny/fate because they are meant to always be together.
...It makes sense in my head haha. I don't think I explained it well though... If you're confused or have any questions or anything, then just ask and I'll try to answer as best that I can.
Thanks again for reading this! This is probably my favorite story that I've written, out of any fanfiction I've ever written ever, so I hope I can write another one soon :)