So, how would they "transfer" the cosmetic slots to new Clone Engine's country? Like, how does that work? Could you theoretically, transfer, say, one of Wario's costume slots, to someone like Mario? Or is it sort of an isolated situation? Finally (I know I'm asking a lot), but do you know why those isolated few characters have extra slots after the standard 10?
There wouldn't be any transfer involved, per say - those slots aren't actually assigned to any character. They're just plain empty, and happen to exist after those characters. Let's take Ganondorf as an example.
Ganondorf's Battle Portrait numbering starts at 191. Normally, the next character's numbering would start at 201, which means you'd have to stop Ganondorf's costumes at 200, which would give him ten costumes.
However, for whatever reason, 201-210 don't belong to any character at all. They are empty. Personally, I find it likely they were meant to belong to a cut character. Whatever the case, this means you can keep on adding costumes to Ganondorf without worrying about hitting another character's numbers.
Or, it's possible that PMBR could create a new character and place their cosmetics in those ten slots. They did so with Roy, using an empty slot that existed after Wario's second slot.
Giving them to any other character would require a lot of work since they don't come directly after the other characters' slots. With Ganondorf, you're just counting up from his naturally existing slots. With, say, Mario, you'd be specifically coding to have him load from one of these slots for only one costume and none of the others, and I'm not even sure if that's possible.