Well, that's where the "imagine" part comes into play. That's all. You're right on the calculations though.
Let's do it again: Nibali had 38 seconds on Mosquera prior to stage 19. Imagine the Spaniard did not concede any time on stage 19. That's 38 seconds going to stage 20.
At -1 kilometer, on the Bola del Mundo stage, Mosquera had 20 seconds on Nibali. If we do the math: 38 - 20 = 18 seconds. Let's say, for the heck of it, that someone ended up the stage between Mosquera and Vincenzo, meaning the Galician would get the 20 second time bonus and Nibali would get 0 (I don't think there was a time bonus for 3rd). That's 18 - 20 = - 2 second to Mosquera, making Ezequiel the winner of the 2010 Vuelta.
That's gotta itch like a bítch with STDs.