I was afraid it might really be something like that, so I never check that box off thinking it might overwrite something I already use. This seems like a confusing place for this, or at least the way it's presented seems confusing to me.
@SentaiBrad, I don't have a screenshot right now but you can't miss it if you just import a game by drag and drop and look at the last item where you select which art you want (like box front, clear logo, etc).