You can't say for certain since these things are quite opaque but I am fairly certain that taking calculus and other such classes in high school is not positive

You can't say for certain since these things are quite opaque but I am fairly certain that taking calculus and other such classes in high school is not positively factored into admissions at elite universities. In general those would not even receive credit. E.g. at MIT you can get, at most, credit for calculus 1 if you get a 5 on the calculus BC exam - AB is no credit. Elite universities tend to try to make admissions somewhat objective and so you get certain points for various things. And coming from a less privileged background gives you a pretty big boost. Pair that with a perfect SAT and you're already very near the finish line. Really strange he wouldn't get accepted. Extracurricular/sports are also important. I came from a crap school, went to an top university (and did not have a 1600), felt slightly behind early on in calculus since most of everybody had already taken it in high school and I had not, but the playing field leveled out very rapidly. Never felt the least bit disadvantaged in any other course. I'm also certain that I would not have gotten in if I had my exact same background but came from a more prestigious/wealthy school. Of course I'd probably have done more in my high school years if I had that background, which is exactly why you get that boost coming from a poor background.