Lets take BU as an example. They charge what, $100 for processing a secondary? Lets say they get the 8,000 applications you propose.
For arguments sake, lets say that their computer has, unbeknownst to them, and prior to even sending out the secondary, already screened 50% of them out because of their MCAT, GPA or both. I would argue that the number is much higher than that, but I'll go with half to account for the fact that some students are not even in the right neighborhood and shouldn't even consider applying to that school.
So that means they're making $400,000 off of people whose applications will NEVER be seen by human eyes.
Clearly, they do NOT look at all the applications. I don't know any other business where you are charged to find out that you have ALREADY been disqualified.
What does that change? Will it make my application different? Minimally, but yes, it will. I'm only applying to a small number of schools. If I have to choose between two similar schools, and one of them is practicing what I consider to be unethical behavior, I'm going with the other one.
I'm not arguing that secondaries shouldn't have fees. I'm saying that if you're going to do a pre-screening, like I am absolutely convinced they do, then you shouldn't rip people off.