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.