Now that there is conditional logic available in the Populi application form, there should always be conditional logic available to apply to the application fee using codes. The problem is that the app fee is in the "Settings" area of the application and not a field. Even still, there could be a bank of waiver codes that, when present, automatically waive the app fee.
In the enrollment world, this is a basic tool we use during recruitment to drive applications. When prospective students are given an app fee waive code, they are then empowered and encouraged to submit their application sooner. If we are only able to waive the app fee manually, there will be prospective students who complete the application and won't submit it. Yes, we could go in and do the hard work to find them and waive the fee manually, but the spark is gone. There is something special about an Admissions Counselor or Recruiter giving you a waiver code and saying "now your application is free" that DRIVES them to submit the application. This is a very basic concept in the enrollment world and exists on every other CRM and application software, even basic HTML form options.