Oh, you're supposed to be given just the shoe swab, not the full secondary treatment -- but as we know, all too TSA officers love to make up all sorts of nonsense rules on the spot and abuse their authority, so there is no guarantee that TSA officers will actually handle things the way they are supposed to. There are plenty of TSA folks out there who seem to enjoy giving retaliatory secondaries for all sorts of reasons, including to people like you who decline to take their shoes off. That said, my experience has been that usually the TSA has given me just the swab, not the full secondary.