Well, I don't think secondary fees are as "nefarious" as some people assume - Yes, most medical schools do not have huge recruiting/admission budgets, and many use volunteer time (including my school). Indeed, there are significant opportunity costs involved in admissions. But I think there is no way collecting these fees would even put a dent into those costs.
If I was designing an admission strategy, I would be loath to have two screening passes. I know for a fact that great candidates sometimes don't have great numbers. And Vice-versa. If I was really acting in the interest of the school, I wouldn't use a numbers-based pre-screen.
No, unless you are doing a straight numbers-based "pre-screen" you are going to have to a human being crack open the application and read it. Sounds like a logistics nightmare to me at that stage: Why? Because if you are going to assign a busy physician or scientist an application, physically or electronically send it to them, and have them open up and write up a formal report or something else- you might as well have them read it in its entirety and make an interview invitation recommendation.
So - if you are like me and loath to use straight numbers to screen, and you recognize that there is little time/money "saved" by pre-screening - what can you do? Why, a fee, of course. Think how many people would apply to every school if there was no additional cost. With no "down-side" people would apply to EVERY school. That's no good.
Having a nominal fee prevents the adcom from being inundated with applications. It is ideal? Nope. Sure there are waivers for people who qualify. But waivers require additional effort, and that's probably not fair. But the fees are a proxy for pre-screening. Think of it as the alternative to a pure numbers-based screening tool. It is sort of the lesser of two evils.
Now that's my two cents. I might be off base. Would I pay the fees again even knowing I was rejected a bunch of places? Absolutely. At least I was given a shot - however slim. Better than auto-rejects.