Admissions at highly ranked colleges and universities in the US is very difficult or perhaps impossible to predict. Merit is important, but admissions is not strictly 100% based on merit, and merit can itself be subjective when kids are applying from a range of high schools with a range of course rigor. Universities are looking for students who are a good fit for them, and it is hard for us to predict what they think might be a good fit.
Just as one example of how arbitrary this process is, years ago the Stanford alumni magazine included an article on admissions. One example they gave involved a tuba player. The Stanford “marching” band (they have a loose definition of “marching”) needs a tuba player. In years where their tuba player is graduating, they might give preference to a few students who play tuba, in the hope that at least one of them will join the band. In years where the tuba player is a lower year student and is planning to stick with the band, they might not give preference to an applicant who plays tuba. How are you as a parent going to predict this? A: You don’t.
In my experience at highly ranked universities, the students came from a huge range of high schools. There did not seem to be any advantage at coming from a rigorous top tier high school. I did know one student at MIT who, if I am remembering this correctly, was only 7th in his high school class (out of about 500 students), but who had come from a very well known very rigorous high school that specializes in science and math. 7th would not have gotten a student admitted from most high schools. However, if this particular student had attended high school almost anywhere else, I think he would have been ranked higher than 7th out of 500 students.
A wide range of things can be considered a good EC. Taking care of a younger sibling or having a part time job is a good EC.
My freshman year roommate at MIT had attended a terrible high school, but was the top student in his high school. Excelling at an ordinary high school might get a student into a top college or university, but again this is difficult to predict.
Being deferred is not the same as being rejected. Top schools in the US do indeed mostly have holistic admissions, and you cannot accurately predict results.
You are going to need to wait and see how this comes out. However, your son absolutely positively needs to do two things (unless he has already done both). One is to get applications into other schools. The other is to understand that strong students can excel and can get great opportunities at a very wide range of colleges and universities.
If you do attend MIT or Stanford or Harvard or a top LAC, after graduation you will find yourself working alongside graduates from a huge range of colleges and universities, and no one will care where you got your degree. If you go to a highly ranked graduate program, then you will find yourself studying alongside students from a huge range of colleges and universities. MIT graduates routinely work alongside UNH and U.Mass graduates and no one cares where anyone got their degree. Sometimes a U.Mass graduate solves the really tough problem that had stumped two MIT graduates (and yes I was one of the MIT graduates who was stumped in at least one case). Sometimes the U.Mass graduate is also a great guy and you go to lunch with him after he explains how to solve the hard problem.
If your son is competitive for a highly ranked LAC, and if he has applied to a good range of schools including two safeties, then he will have a good school to attend in September.
The school cares about whatever it cares about, which probably includes finding students who are a good fit for them. If your son doesn’t get in, then he will get in somewhere else, and somewhere else will provide him with great opportunities and a strong education. Also, if your son does not get accepted to this one particular school, you will probably never really know why.
There really are hundreds of colleges and universities in the US which can provide a great education. Make sure that your son applies to at least one and preferably at least two where he will be accepted, and that you can afford to pay for. This will work out one way or another.
And support your son through this process. However stressful this process is for us parents, it is more stressful for our kids.