Chances are, it's the best the regulator manufacturer has to offer, rather than the best for the service. Chances are a PFA or metal diaphragm are just plain not flexible enough for the service, even though they're both probably less hydrogen-permeable than the diaphragm he's suggesting.
Most materials are permeable to hydrogen. But at low pressures, EPDM is probably good enough. All depends on how "low" is "low" in your case.
Lower perhaps, but probably not by an order of magnitude, so do you care?
If you have the thickness of the diaphragm and the permeability you can calculate the rate of permeation. Probably not enough to worry about, provided the regulator is designed to vent any diaphragm leakage. But then again, what happens should you ever have a diaphragm failure?
