He added all those clubs just in this school year? Are you forgetting any collaborative math-sci ECs in the school, among his own hs peers?
The diversity issue is so many strong aplicants from the Bay Area. Most colleges can’t accommodate more than a smaller number from a particular sub area.
You’re going to need to see what the GC says, whether he or she feels this is competitive from his hs. After that, it’s up to adcoms. A lot of kids will apply with top stats and the right variety of activities.