If the conf champ doesn't have 10+ wins, that conf auto bid transfers to at large for that year and the conf champ has to compete in the at large pool.
Otherwise it would allow too much wiggle room for someone like, say the SEC, to game the system and get 3 teams into the playoff. Just imagine a year where Bama is 12-0, LSU is 11-1 with only loss close to Bama and the SEC East rep is an 8-4 Kentucky. Bama throws the championship game (or even has a legitimate down day while resting some key players). 9-4 Kentucky gets auto bid and 11-1 Bama and 11-1 LSU snag two at large, UCF qualifies for a mandatory at large by being unbeaten while playing no one and cracking top 12 or whatever and 11-1 or 12-0 Notre Dame is left out.
The auto bid for conf champs is a very bad idea, unless there are some additional qualifications that must be met (ei conf champ and 10+ wins). If you leave room to game the system, someone WILL take advantage of it and with five auto bids and only three at large, the chance of lesser teams getting in over more deserving teams is too great.