Technically, a downloaded game that you pay for is retail
Actually, no. Retailing implies a physical location. And, yes, it is different. You have quite a few major differences like having to manage shelf space, as opposed to online stores which don't have to worry about that. But, the author of the article made a poor distinction and the discussion will be muddied.
As for preferring a boxed version, I don't generally care either way. I am not concerned that GameStop and ilk will maybe go out of the gamer-gouging business (although they've made huge inroads into digital distribution). However, I am concerned with the loss of one of mygames. Should Steam go belly up, whence go my games?