They have been determined on an equal playing field to be the best in their leagues. A playoff, then, should determine which of those champions is the best in the country. So a model like this would be ideal...

All 9 conference champions get auto-bids plus the highest ranked independent school, provided they rank in the top 25 of the CFP rankings. So 10 schools.

Two highest ranked of the 10 get double byes straight to the semi finals.

The other 8 are seeded according to CFP rankings straight up and paired.

The 4 winners go on to face each other in the next round.

The 2 that win those games go to the semi finals where they'll meet the top 2 teams.

This kind of system would give everyone a fair shot at competing for a title. No one is left out. If you aren't the best team in your own conference, then you have proven that you are NOT the best team in the country, so no need to have you in a playoff.

Of course, this will never fly because TV people want big brands over G6 champs in the playoffs. So that leaves you with the next best alternative - which might just be guaranteed slots by conference, but the conferences can create a playoff scenario within their conferences to qualify for those slots. This helps make sure all deserving teams get a fair shot at playing their way in.