I just came across a variant in the wild -- a Quora comment -- which puts the noun as the thing to be explained rather than the explanation:

That was the point if the question, though. "If God does not exist, then how come physics?" And the answer is, "You can just leave off the 'God' part and just ask 'how come physics?'"

I wonder why "how come [noun]" is recognizable as sort of the same thing.