I've come up with a theory about how some Sonic fan universes interact with one another, and how characters can travel between them. Below, I'll outline that theory, for the edification of anyone interested; all my characters and fanfics will abide by this theory, and anyone else who wants to is welcome to use this theory for their works as well. (This theory will probably evolve over time. Feel free to comment with suggestions.)
Areas of three-dimensional space which constitute closed systems to the standard laws of physics, hereafter referred to as universes, coexist within a larger quasi-dimensional field of being, hereafter referred to as the multiverse. The multiverse contains many universes of varying sizes.
When there are similar locations in multiple universes, those parts of their respective universes are close in the multiverse.
For example, a city and its alternate-dimension counterpart will be very close.
It does not matter to the multiversal closeness of things if Point A and Point B are adjacent in Universe 1, and Point A! and Point B! are very far apart in Universe 1!. The multiverse is not a conventional space, and as such does not have to abide by normal rules.
High concentrations of scientifically impossible occurances, hereafter referred to as magic, can cause localized weakening of the fabric of a universe.
Universes naturally repair themselves over time, but extreme magic use during a relatively short period of time over a large part of a universe can cause its eventual utter destruction.
Where universes are close together, and one or both becomes weakened, they can touch and open a portal to allow passage of matter (including people) between the universes.
Powerful magical artifacts and/or concentrated applications of magic could be used to open portals between known close spots in different universes.
Inter-universal collaboration could produce pairs of identical loci to make otherwise distant parts of two universes close together for the purpose of opening portals.
Magic-dampening bulwarks could be emplaced around common portal sites to contain the universal-fabric damage to a small area.
Chaos Control is a mysterious magic so unscientific that it rips the fabric of the multiverse itself to translocate the wielder between distant places, whether within or between universes.
I developed this theory over the course of a long conversation with Wikikinetic and another person (who is not on the Sonic Fanon Wiki). They each contributed one of the possible applications and helped me flesh out bits of my original theory.