First, USAFA does not have a waitlist. It's simply an offer of appointment or no offer of appointment (although the time you may wait to hear back differs greatly among individuals). USAFA selects candidates that are both qualified and competitive, while those not selected are not competitive for an appointment.
This is the pool the Falcon Foundation has to choose from, and (from what I understand on their website) they "rack and stack" them from this point. Realistically, they are not going to choose someone from the bottom of their list or arbitrarily pick a person strictly based on the high GPA/average test scores combination. There are many other factors that go into each candidate's ranking, such as leadership experience and ECs. This is reflective of the whole person concept, similar to how USAFA chooses its appointees. I'm not sure anyone outside of the Falcon Foundation has the specific formula, nor do I believe that analyzing it is worth the effort. But again, there IS a method to their madness, which is why/how candidates are "rank ordered" for the scholarship opportunity.