The amount of time Phonak would lose would not be enough for Kloden.
According to the excellent Lance's Armstrong's War (which I am reading now).
Back when Discovery was strong, they put too much time on the other teams in the TTT. Ullrich lost 1:01 in 2003. In response, in 2004 the tour socialized the scoring, so that the second place team would lose only 20 seconds, the third place team 30 seconds, the fourth place team forty, and so on. According to Coyle, the TTT effectively gave the weak teams the day off. Phonak wouldn't take the day off, and likely wouldn't be so far down as to endanger the 1:29 lead Floyd now enjoys.