Do you make that same statement about the Super Bowl, and the NCAA tournament, where there could easily be cases where the winner had been previously defeated by the loser.
The NFL and College Basketball require a team to win their way into the championship game through a playoff system. If the NFL used the Bowl system Green Bay would have never been invited to the Superbowl last year, it would have been the Patriots vs the Falcons...........but somehow neither made it that far.
If Bama beats LSU tonight, then what? Since LSU already beat Bama, each could claim the BCS Championship, since each would only have one loss - to each other.
There are many situations in sports where each team could have one loss, to each other, but only one win a championship, or advance in a tournament. That was the point you made and it is a fairly ridiculous point because the situation you describe is so common.