Lance specifically said before today's stage that if Alberto attacked, he would sit back and defend the other contenders as a good teammate. We do NOT know what Lance was holding back, if anything.
Also being a good teammate, Lance did do more work in the TTT than Contador.
Being behind, even by 2 seconds, is a big disadvantage for Lance, but that's what the team has done. They wanted Lance in yellow after the TTT, but missed by a hair. Most everything else is according to team plan.
The earlier point about the opening TT is valid - conditions could have easily changed in the time between LA and AC.
The last TT is longer and flatter, which should work in Lance's favor versus Contador. He'd better hope so, because the final TT may be his only opportunity to get ahead.
Even if he wasn't red-lined today, it isn't likely he will
a) get the go ahead to attack Contador, and/or
b) be able to drop Contador in the mountains.