Whether it’s a deferral or a rejection, anything can happen to a single application. I don’t see anything in your profile that suggests Columbia was more of a reach for you than for most applicants.
Not entirely sure how to submit recommendations through the CA - my school uses naviance - but your GC can probably help. As for schools allowing 3 or 4, they still tend to prefer 2 teacher letters, for reasons I outlined above.
Hopefully, CMC and USC won’t care all that much - CMC has fewer applicants than places like Columbia, so admissions officers may be able to read through a longer application, while the UC’s are primarily stats-based.
UChicago indeed - class of 2020 or bust. Good luck.