Note that there are no transcripts on application – applicants self-report courses and grades, to be verified later with final transcripts for those who matriculate. This substantially reduces the data entry work at the school, since it is effectively offloaded to the applicants.
At least at Berkeley, the process is something like this:
Each application is read and scored (on a 1 to 5 scale, with 1 being the best) by two different readers. If the scores differ by too much, a third senior reader scores the application.
Then all scored applications are ranked within division or major as applicable. The cutoff determined by the number of admits desired (which is presumably determined by the estimated yield) will fall at some score level. All better are admitted, all worse are rejected. At the threshold score level, tie breaking procedures are used to determine admit or reject decisions. Note that there is not a small central admissions committee reading all of the applications and becoming a bottleneck in the process.
Recruited athletes are run through the usual process with no special consideration (though the sport counts as an extracurricular, of course). Those who are not admitted through the usual process are considered for the spots reserved for recruited athletes.