Well, the easiest way to say it is that she did it in all worlds simultaneously by granting “Miyoko”'s wish. Because the miyoko in all those similar worlds is Miyoko, then by virtue of that her wish could easily be granted that way.
Also, well, its hard to say but it could be interpreted that worlds branch. Plus its not exactly a perfect metaphor granted the witches are running around it. It gets complicated by it. Its a decent enough example though on a basic level without the witches existing in it since its not accounted for. It could just be that a gameboard produces fragments with a similar setup to the original. Perhaps theres a sub-alpha fragment that acts as the base for the gameboard like one could say rokkenjima prime acts as for Umineko.