It actually can be (and is) waived for certain platforms. I stashed in anthro while in A-pool and was the one that printed off the "waiver" or statement of understanding form. I forget now, but you either had to be anthro eligible for one or two platforms. We had everything from small females who's arms weren't long enough for reaching all the necessary switches and buttons in certain cockpits to guy's who's ass to knee length put them outside the envelope for a safe ejection in the T-45. The later was the most common. My boss used to rant about how the Navy bought a British aircraft that was designed for the slightly smaller British stature. The "waiver" was a form the SNA would sign acknowledging that an ejection from a T-45 might kill them. The anthro tolerance for fleet aircraft after winging from the tailhook program was larger and the pilot/NFO usually would not have to worry about ejection issues anymore. Occasionally, they would put an SNA/SNFO in the actual fleet aircraft's cockpit and made sure they could perform any button mashing/egress that might be necessary. I personally never saw someone anthro'ed out of aviation completely, although occasionally someone was only eligible to fly a couple platforms.
The guy that made the final call was a flight physiologist. The one I worked for was a prior prowler NFO.