My D20 looks very similar to your S on paper, just substitute baseball for another sport and replace theater and MUN with all of the orchestra-related offerings you can think of. Our school calculates gpa on an unweighted 100-point scale, our list of schools has a lot of overlap with yours and we had a fair amount of financial need, too.
I am sorry you are disappointed by the responses he has received and I understand trying to second guess what went “wrong”. I agree with Naviance not offering a full picture, admissions being more holistic than the 2 stats tracked on it, and it is hard for us to understand why everyone doesn’t love our kid. I’m not sure when the RD decisions come out from his deferred schools but if it’s not too late, he could reach out and reinforce his interest in attending.
Hang in there!