Correct. Only conference champions can get the byes. Notre Dame will top out in the 5 v. 12 game when they have a great season and that's perfectly OK w/them.
Doesn't that lead to a future problem because of divisions? Say a 9-3 USC beats 12-0 OSU 21-20, they get the bye over OSU even though OSU won over the regular season 42-10? Or a bye over 12-1 Alabama who only lost to 13-0 Georgia?