Most of the problems we class as "metaphysics" probably aren't empirically verifiable, but if a few turn out to be, it isn't a big problem for the positivist program. Their objection to metaphysics isn't as principled as you make it out to be. It just falls out of verificationist semantics.
So if a physicist manages to empirically verify a few things that might have seemend metaphysical, then cool, turns out they were doing physics not metaphysics.