I’ll send you back to your son for specifics. I am several years removed from my time on staff there, and while I know the general policy and can look at the written guidance, how it is actually being administered is nothing I have visibility on. I am sorry I can’t reliably advise on those details.
The true bottom line is if you are in the military, you are expected to maintain a certain level of fitness. Working out regularly and ensuring competency in tested areas is expected of midshipmen as well as admirals. Lifelong PT as part of daily activities is part of the culture. And for officers, you are expected to set an example for your people, not be struggling to pass. When I was on AD, I knew any PRT failure was essentially a career-ender or at best a blot that could never be repeated. If a midshipman has trouble doing this, it does not bode well for his career. USNA takes steps now to address that, and the midshipman either overcomes the problem or is not deemed to be suitable for service as an officer.
And asking this with respect and concern for your son, is there any chance he does not want to be at USNA but has not permitted himself to actively explore leaving because of some pressure he has put on himself or concern for family? It is not uncommon for midshipmen to realize perhaps USNA is not their place after all, but can’t quite steel themselves to articulate that for fear of disappointing others, so they unconsciously allow themselves to slip academically or in the PRT, so that USNA makes the decision for the midshipman. If a midshipman has tried and given good effort, but realizes this is not their path, it’s not quitting, it’s choosing to go forward on a new path. This is why a midshipman can leave the first 2 years without incurring obligated service or having to repay the cost of their education thus far. I only bring this up because it does happen.