The points I see missing from that very accomplished young man's application to these top schools are the essay(s), any interviews he may have done and any sort of philanthropic or leadership roles he may have been involved in. These are all important, now more so than ever.

It is entirely possible that he did not demonstrate, through these other avenues, the desired qualities of a student from the schools he was rejected by. Getting into such schools isn't simply a matter of racking up points by following some formula and quite a few kids do not seem to realize this.

When a school has a flood of equally polished test scores and fantastic accomplishments it can result in other criteria playing the deciding role. Perhaps he didn't meet these other criteria? They are not discussed in the article so no way to know. I personally suspect this, much more than mere ethnicity, as I know they matter greatly in the application process at such schools.