@KC2022: This is why, for so many years (when I had more time/energy for this sort of thing!) I preached the gospel of the wide net. 2 schools is really not enough…and even more so if the schools are among the most selective (the so-called “HADES” type schools).
I think you may have also been distracted by your son’s 99% scores. The most selective schools turn away dozens of 99%-ile scoring kids every year. It is no guarantee of admission or even standing in an applicant pool.
I think your final sentence of post #35 above is key: “in the end the selection seems more arbitrary than merit based”. If, given more similarly qualified applicants than you have slots for, some of the decisions will definitely seem arbitrary to those outside of the selection committee. As noted by others above, you have no idea what the kid who got admitted brought to the table that your kid didn’t.
IMO, it’s only worth mulling over possible reasons for rejection if you are going to use any insight to help sharpen your son’s application for next year. If going to a BS is important to your kid…then widen the net to include more schools. And if you were focusing only on super-selective schools this year, be sure to include a few less selective schools where your kid will be a real “catch” and not just another well-qualified candidate…