RM would be able to explain much better than me, but here's what I think just based on my own experience from owning one.
You're lying down, elbows over the handlebars so the top tube is shorter (like MD said), and the steepness of the position changes the whole "cockpit" measurements (what my LBS calls the top tube, leg, reach measurements, etc).

My DH rides a 56 road bike, but won a 52 TT at a triathlon a couple years ago and they were able to fit him to it (and quite comfortably).