Some good points and some arguments that PDs have been using for years that completely fall apart under any scrutiny.
In the case you mentioned, that's close enough where those factors do come into play, but it's also not what we see in practice. In reality there is a much bigger gap than that in terms of performance vs. placement. The real argument you can make for Columbia vs. DO school in close cases is that the Columbia guy likely has a track record of success longer than 4 years while the DO guy more recently got his act together. There is something to be said for the idea that anyone can study their ass off for two years for that perfect step score.
That's about where the valid complaints end. Honestly, most people are functionally useless when they start internship. You might have some book knowledge and familiarity writing notes and talking to patients, but that's about it. Medical school training is very necessary, but doesn't change that much from school to school because you're never really in charge of the patients and the quality of training is more dependent on the attending's teaching skills than on the environment. Maybe the guy who's used to the big academic center has a slight edge, but not much, and nothing that wouldn't be functionally obliterated in the first few months, when everyone is adjusting. Not to mention, with the type of discrimination we're talking about, it's not Columbia vs. DO and totally different training environments. It's Columbia vs. OHSU, and a med student will hardly even experience the functional differences between the two while working there. The track record of success argument falls apart too, because med school admissions are a crap shoot, and the difference between a top 30 student and a top 10 student is very often luck and circumstance. Same goes with top 30 vs. top 50, top 50 vs. low-tier MD, etc...
None of this accounts for the huge differences between the match list of a top 10 vs. a top 30 vs. a top 50 vs. any MD school vs. any DO school. A top 10 will have virtually all IM matches and nearly all other matches at top universities. A top 30 sees a few fall through the cracks. A top 50 will be lucky to send one guy to a top residency in competitive specialties, and even in IM they'll send 1 or 2 to top 10 programs. Low-tier MD schools send the vast majority to community programs, and DO students are lucky to get the specialty they want at all. That's a steeeeeep drop in match quality as rank goes down.
So while you mention real concerns, it simply doesn't hold up to the level of discrimination seen IRL. Top programs certainly know they're robbing themselves of higher quality residents by not choosing the top students from a number of schools rather than mediocre students from top schools, but ultimately it's about pleasing the chief and making the program look shiny on the outside.