...if you try to exchange in store you're likely to get a brown box unit. Those are just the phones on their own in plain boxes for warranty replacements. It means you won't get one in retail packaging off the shelf and your new phones serial number won't match that on the original retail phone box.
I'm not sure that matters does it? How many buyers of a 2nd hand iPhone would cross-check the serial number of the phone with the box, and anyway, if asked the "Genius" would give you a sticker with the new serial number to put on the original box covering the original serial number.