Okay, there are two different conversations going on here and I think for the most part the point is being missed in both of them.
Yes, people get into schools with a 3.5 GPA and 28 MCAT (AND is a key word here, italicized in the OP, meaning both those things at the same time. Those 3.4s that make the avg 3.6 also likely have a stellar MCAT score.). They do get in, but at a rate of only 29% of white applicants, slightly higher for URMs. AAMC table 24, folks.
What this means for OP's question, is that, in all likelihood, applicants in that range and below are also applying to schools they have ~0% chance of getting into. Hence, 3.5/28 is in fact a "junk application" at those schools. Not at all schools, but at many. Those falling within those stats shouldn't be offended or upset by this fact, just let it guide you to not throw your money away applying to schools which will not accept you.
So, at these schools with 10,000+ applicants, according to the adcom members here, the generally strong applicant is really only competing against ~5,000 people. That's...ummm... a relief, I guess? 😉 It's actually about what I was guessing based solely on my understanding of people in general (see goro's point about faculty job applicants).