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The school you apply to really doesn't affect your potential admission (unless you're applying to Shepherd or the architecture school). The admissions office knows that a large number of students are going to end up graduating in a different area of study than the one under which they applied. Having you apply to a specific academic division is just to make sure that one department doesn't get overwhelmed. There aren't any real "quotas," and one academic division is not easier to get into than another.
If you are actually planning on studying in natural sciences, then you should apply to the school of natural sciences. It will save you some headaches with academic advising during Orientation.
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