Although we are also struggling with decision making (at a lower level than you - Berkeley vs UCSB CCS Physics), the safest option seems to be Caltech. Caltech provides most of what he is looking for in Physics along with CS (theory). Caltech CS versus CMU Physics, we feel that Caltech would win there. The CMU physics has nothing exceptional to it. My son is hardcore into Physics and CMU was not in his list of 10 schools he applied to.
However, the real answer need to come from your son himself.