DoDMERB does not waive. All they do is determine if the candidate is medically qualified according to the commissioning source, in this case AROTC. AROTC decides whether or not to waive the condition.
I do not what he was DQ'd for, but as an example if it is for a learning disability and being on Ritalin, passing the APFT has no impact on that condition. If it is asthma, they may request additional exams.
The waiver is a big picture issue, and as hard as it is to read, it really is not just about him. They are looking at if they can be deployed, especially in war time. Additionally, think of it like a preexisting condition regarding health insurance, the military is accepting the preexisting condition and will cover all medical issues/costs associated with the condition.