According to my former roommate who is a Navy FS and FAA examiner (OK, was as he's an anesthesiology resident now...), he CAN NOT give a FAA physical unless it's on the side, and he's set up to get all the paperwork/EKG etc. to OKC...which basically means having his own practice, which the Navy won't allow....
Back in the late '90's they could, but someone got ****y about it and wrote the prohibition into the CNAF instruction.
HTH
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