The waiver process is only initiated for candidates that USNA would give an offer of appointment had the medical issue(s) not been a factor. Even being triple qualified plus a nomination is not a guarantee of an appointment (or entering the waiver process, for those who are medically [2Q] disqualified). So what I am basically saying is that when the waiver process is started, USNA has already determined that if your medical issue is found waiverable, the chances of receiving an appointment are good, mostly contingent on the grant of a waiver; though again, nothing in this process is guaranteed until you receive official notification of an appointment.
Also, let's not confuse the actual waiver process. A waiver being granted DOES NOT have anything to do with a nomination, rather it is a thorough review of each candidate's medical file by the USNA medical staff, which normally is also reviewed by Navy's Bureau of Medicine, and a recommendation is then sent to the Superintendent for a final decision.