The typical "overqualified" tag is not necessarily true for the Falcon Foundation Scholar program. My son is currently a Falcon Scholar at MMI. He had very good test scores (above the mean in both areas), but his GPA in H.S. was not that great. He also had excellent leadership, sports, service, etc. I think the bottom line is if you have strong academics that may bump you out of the USAFA Prep school, they may offer you a Falcon Scholarship instead. At MMI, there are Falcons with CFAs that need improving, SAT/ACTs, etc.
I also believe it is different for each academy. When we went to CVW at USNA, they specifically said they either put you in the prep offer category or you are just considered for direct entry.
The letters for Falcon Foundation go out in February. It is a great option if you don't get an appointment the first time.