a [box [of apples] ] vs [a box] [of apples]
One generally assumes that only constituents can be replaced by an indefinite pro-form and that only a constituent can be the antecedent for such a replacement. So since we can go from
I want a big box of apples, but my sister wants only a small box of apples.
to
I want a big box of apples, but my sister wants only a small one.
then "box of apples" must be a constituent. This rules out the structure: [a (Adj) box] [of apples]. It must be instead: a (Adj) [box of apples].