I'm not really familiar with the topic matter here, but I want to note that Michael Nielsen contradicts what you said (though Nielsen isn't exactly an unbiased source here as an Open Science advocate):
Perelman's breakthrough solving the Poincare conjecture ONLY appeared at the arXiv
The important point is that it doesn't appear that Perelman produced the paper for publishing in a journal, but he made it and left it on the arXiv, which was later (you claim) published in journals. That's quite a different view than "if it's not published, it's not science"
Indeed. However, you've raised a single remarkable exception to a general heuristic as if a single example is all that is needed to thorougly refute a general heuristic, and of course that's not the case.
The overwhelming majority of papers put on arXiv and nowhere else are:
Recently, I gave some reasons for SIAI to begin publishing in mainstream journals, and outlined how it could be done.
I've recently been made aware of some pretty good reasons for SIAI to not publish in mainstream journals, so here they are: