Numerous bowls will go with rankings before conference runner up. For example, the Big 12 in 2005 had Texas win the Southern division and Colorado won the Northern. Texas was 11-0 at the time and #2 in the country. Colorado was 7-4 and not ranked. The Big 12 Southern divison was vastly superior in 2005. Colorado would have come in 4th place in the Southern with their 4-4 record.
They went on to lose to Texas 70-3 in the conference championship game.. Texas, obviously, went on the play USC in the champioship game. Texas Tech (who finished 2nd in the Southern) was picked to play in the Cotton Bowl. Colorado went on to play in the Champs Sports Bowls.
I always though the conference divisions were made in an effort to set up a conference championship game...and not to be a bowl picking system. I like the rankings criteria that these bowls use. It helps avoid situations (like above) where one division is much weaker than the other.