As a prospective physics major at Columbia College, I think that you should apply to CC if you are really interested in theoretical sciences (eg, physics, chemistry, biology) as long as you are ok with taking 1-2 humanities classes (the Core) every semester. Unless you are dead set on engineering, I don't find any reason for you to apply to SEAS instead of CC. In fact, CC has heavier core curriculum requirements than SEAS, so it may be harder for someone in SEAS to transfer to CC than vice versa (assuming that you have fulfilled the basic major requirements).
I can't speak for junior/senior year courseloads accurately, but CC students will definitely have to take more core classes than the SEAS counterparts (who will likely take more intro science/ pre-professional classes as their "core" - which differs from the traditional CC core classes like Lit hum and Contemp.Civ). Although SEAS students take slightly more classes than do CC students, it usually depends on the student's ability/willingness to work hard. Generalizing is difficult in this case, since some CC students manage to take 6-7 classes while a few SEAS students take only 4-5 classes.
Looking at the admissions rate, CC has a slightly lower acceptance rate than SEAS. But, that may be due to a higher level of self-selection in SEAS (not many people apply to engineering schools). And as far as I know, CC degree is written in Latin whereas SEAS degree is written in English.
Hope that helps