For the purposes of key generation, however, wouldn't you want the full n bits of entropy? Otherwise the search space for a brute force factorization (haha right) is 2^(n-1) instead of 2^n, or half as many possibilities. The domain of the product is still [0..2^(2n)] so the resulting key is the desired 2^(2n) bits.

I guess another way to pose my question would be: is there an issue with sampling the entire 2^n space that makes us only take the highest 2^(n-1) subset of integers instead when selecting factors for a key?