As it says in the second message, those are the best-run programs. Of the ones there that I saw, I'd agree. And there's no real proof of that. Those administrations are just known for being on the ball throughout the circuit, their students sing their praises, etc. But administration is only part of the equation.
You could make a separate list of places that represent the best academic pedigree, those best known for producing students focused on research and academic medicine, etc., etc.
There's no magic formula for an MSTP. I was less than impressed with some of the schools (even on that list) where I'd been told to look forward to my interviews, because there was one thing that would have driven me nuts had I gone there.
So in my opinion, you're out of luck with the rankings game. No numbers will guide you in the right direction. They're little, focused programs, each with their own quirks... more like a small graduate department in the liberal arts than something like a medical school class.
On the bright side, you don't often run into people who are sorry they enrolled in their MSTP.