Like Crayola227 said you'll have to identify which schools accept the FAP and which schools do not. For example, in the MSAR Howard is listed as having no fee waiver eligibility while Meharry accepts it. And the FAP only allows you to designate 16 schools which would mean if you're going to apply to 40+ schools, you would be paying the difference.
Waiver for all AMCAS fees for one (1) application submission with up to 16 medical school designations ($730 value), submitted by December 31, 2019.
Additional fees will be charged for each medical school designation beyond the initial set of 16.
You get a fee waiver for 16 schools on your AMCAS application, so you'd end up paying for the rest. Secondary wise its on a school by school basis. The only schools I paid for were Baylor (50% off) and Maryland (full fee)