Pointing out that a bias exists is not always a call to eliminate that bias. The fact that merely requiring an application rather than being the default option improves average outcomes isn't a problem that needs to be solved. It's just something that should be kept in mind when comparing schools.
At some point, some school is going to have to take the kids who don’t bother applying, since we can’t put 100% of schools behind an application and preserve its benefits, and we should not be surprised that such schools do worse, if the ones who do apply happen to be better.
There is bias in everything, but at least they aren't adding more than needs there needs to be.