The AP were (are?) mindless cattle, stacking up the teams in the preseason, then lining them back up each week according to that list and who lost. The final AP poll is a history of simple minds - undefeateds listed first, then the 1-loss teams, then the 2-loss teams. The only ones breaking the line were mid-majors who were further down.
Personally, I think it's great that the committee had a 2-loss team ranked over another P5 undefeated. The specific schools are irrelevant - it shows that they're not mindlessly ranking the teams the way a 7 year old might. Now, they might've been right or wrong in doing so, but at least they were using their adult minds.
It's progress.