The only way that I can see them being right is if they mean the raw data that the tower gets may be in degrees true; then they convert it to magnetic for the pilots (except in extreme northern and southern areas where the compass becomes unreliable). Im not sure if Im correct, but it at least makes their answer plausable...still wrong in context though.
But no, you are correct that what you are given by ATIS and by tower are in magnetic (excepting for the conditions already mentioned)