Hey hey hey, I'm assuming (which makes an ass out of.. yeah yeah) that though the Doctor may be photonically challenged as far as turning his whole body into something swift that carries passengers he has made sure he has complete control of at least one part of himself and can program that part at will. That's why he's such a smug bastard because even though no one is "close enough" to know this he knows it. It's his secret superiority.
I bet there were encrypted files with special scenes during Tinker Tenor Doctor Spy
that we never saw.