Not quite relevant to the story, but your reasoning for deciding that Sinnoh doesn't really exist strikes me as rather flimsy; well, more specifically, your reasoning for including Hoenn but not Sinnoh, which basically boils down to "Well, Hoenn was out when I was originally thinking of this, and I don't like Sinnoh." It's a very arbitrary distinction, which really bothers me when people are trying to create explanations for anything. There is no part in which Hoenn is specifically relevant to your fanon backstory, and in all respects, your reasoning in fact works somewhat better if you apply it to Hoenn as well as Sinnoh: there are just two
regions, which take little space, and one
champion. Why is three regions and two champions more reasonable than two regions and one champion? If anything, I'd call it less reasonable; having just one champion over the whole Motherland makes a good deal more sense than two of the three regions randomly banding together for one Champion while the third has its own. :/ It works in the official canon since there we can assume that there are many regions and they ordinarily each have a separate League and Champion but Kanto and Johto, being particularly close together, happened to share, but it becomes kind of strange, or at least it seems so to me, when there are specifically just
three regions and they are worried about champions banding together to take over.