Every Big12 team finished with at least 2 lossess, due in large part to the "Kansas" factor you listed above.
By contrast, the ACC had two teams with less than two conference losses.
The Big12 had three teams with less than two conference losses.
The SEC had one team that had less than two conference losses.
The other three power conferences had SIX teams with 1 or fewer conference losses, and the Big12 had zero. That's HUGE. If that goes the other way - the Big12 has 3 teams that have 1 or fewer conference losses, and the oher conferences have zero, then the CFP rankings look very different.
I'm honestly baffled by the idea the Big12 got screwed this year. You look at the AP poll, the Coaches poll, Vegas lines, computer rankings, etc. they all say the same thing - the Big12 teams aren't among the top 11 teams in the country.
Honest question - in a "playoff" between the top four Big12 teams (BYU, ISU, ASU. Colorado), and the top four "bubble teams" in the last bracket (Alabama, Indiana, SMU, and TN), how many of those Big12 teams would you expect to win? I think they'd be underdogs in all 4 games.