The empty set is still a thing, even if that thing is empty. Sets are things. Spacetime would still be the set, even were it empty.
I think a better question is "how can an empty set come to have stuff in it?"
We can start out with 0=0. Nothing is itself.
But we can subtract one from both sides, the equation balanced 1=1. Nothing has changed. There is no contradiction.
As long as the system is balanced.
That's the whole idea of "supersymmetry" I think. The idea that maybe our universe exists as a form of particle within another larger structure, and is itself "virtual", existing to collapse symmetrically against it's antiparticle.
It would be the same universe, so really there would only be the one identity of the thing, only one meaning to it and only one experience of it.
And then it would be gone forever.
The point is, if something comes from "nothing" in observable space, we have no basis to say universes don't do the same in "superspacetime"
Granted, the way watches come to exist in nature is through the evolution of a creative species. We also don't categorically know that this is not one of those such insanities, either. The universe contains a lot of insanities.
I can only hope that if this is the case, there is a legal, moral, and ethical structure to prevent the abuse of intelligent life within created universes.