Stanford would definitely get passed over by the Sugar or Orange Bowls, but they've got the Rose Bowl on lockdown if it's Oregon vs. TCU/Boise in the NCG.
The scenario I see playing out (Auburn loses to Alabama but wins the SEC, and MSU is left out):
NCG - Oregon vs. TCU/Boise St.
Rose - Wisconsin/Ohio St. vs. Stanford
Sugar - Auburn vs. Wisconsin/Ohio St.
Orange - ACC vs. TCU/Boise St.
Fiesta - Big 12 vs. Big East
A problem with this, however, would be if TCU is in the NCG, and the Sugar Bowl takes an 11-1 Big Ten team with the first at-large selection. Would the Orange Bowl take 12-0 Boise State to face the ACC champion if that champion is Virginia Tech? As entertaining as that game was, bowls hate rematches of regular season games. This is where an 11-1/10-2 LSU or 10-2 Alabama would jump ahead of undefeated Boise State.
I could see a one loss LSU possibly (although unlikely) jumping a Boise State. I don't think there is any chance (congressional subpoenas would be sent out before the games are played) if a any two loss team jumped an undefeated team.