A downward firing subwoofer can sound different depending on what the woofer is firing at. For example, if placed over shag carpet it will sound different than if placed over tile or hardwood floors.

Primary reflections don't matter as much with subs as they do with other speakers, but at the distance we're talking (ususally inches), it's bound to make some difference.

That's why I like my SVS with its integrated base. No matter where I put it, the first reflection will always be constant.