I don’t think that’s actually how it works. Here’s a scenario where the Big 12 stays at home while the CFP takes place:
1. BYU loses one of their final two regular season games.
2. #2 Big 12 team upsets BYU in the championship game.
3. Army wins out (including win over ND)
4. Boise State wins out.
In this scenario, it’s conceivable that Army and BSU could rank higher in the CFP than the Big 12 champs and the Big 12 would lose their auto-bid.
Remember that the fine print for inclusion into the CFP says that the five highest ranked conference champions get auto bids with the four highest ranked conference champions seeded 1-4. It doesn’t specify conferences.