Hi Birdie,
I didnt get the FAP waiver, but I am pretty sure that the individual AMCAS schools are not obligated to waive the secondary app fee. However, I would be surprised if they do NOT waive the secondary app fee if you have a FAP waiver. Most schools just tell you to send a copy of the AMCAS waiver and they waive your secondary fee.
I'm just wondering if you actually get the waiver approved or if you're just inquiring. AMCAS is pretty stingy when it comes to those waivers.
FYI: at least one non-AMCAS school, NYU, told me that they would accept the FAP as application fee currency.