First of all, the champ games will define byes so the loser in the champ games will be "penalized" for losing in that game.
Second, I don't think anyone has said that both teams in the champ games are guaranteed slots. There is a pretty good possibility that there will be at least champ game loser who will not make the playoffs.
I think the challenge will be when two highly rank teams play each other and to not let a loss in the champ game affect the seeding -- which would be pretty tough. For example, how do you handle the seeding of the loser of 12-0 Oregon/ 12-0 Indiana? To not "penalize" the loser, they would have to be guaranteed a higher seed than the 3rd team out of the BIG assuming there is one. And while doing that you will have to compare OSU to 3rd team out of the SEC or perhaps even to the loser of the SEC title game.
Because the committee will be creating the 1st history of this decision, about the only thing we know is SEC/ACC/BIG/Big 12/Group of 5 "winners" are in and 4 of those teams will get byes and the rest will be creating a possible roadmap for the future selections/seeding.