I think that most medical school ADCOMs want to not favor one school over another, but in the end most classes are skewed in some way. This is complicated, though. Many of the best-testing students who blew away their PSAT then their SAT then had the finances/etc to get into super-name-brand-schools are still great students when applying to medical school. Therefore, you get a population bias towards schools like Yale and Princeton and Stanford, but not necessarily from the school -- from the students that happened to go there. This is the same argument as about Step 1 scores ... were the JHU med students made into supermen or did they start that way? Hard to tell.
Also, geographic influences are just going to happen. IU has an enormous amount of Indiana residents, many of whom stayed in-state for undergrad, and there aren't THAT many colleges in the state of Indiana. So, bias again. Same here at Penn, where lots of students are either from Penn UG, or Haverford, etc.
I'm speaking as a guy who went to a good but largely unknown LAC and ended up Ivy so hey, anything is possible. But be sure to tease out the real reason it looks like ADCOMs are "favoring" certain schools -- it may have nothing to do with the quality of education there.