Giving the conference champs a 1st round bye seemed reasonable at first. Reward the champs over the non-champs. It didn't play out as well as expected. You could make a good argument that tOSU v. Oregon or ND v. uga will have the two best teams playing each other in the quarterfinals. The seeding needs to be fixed.
I still don't see an issue with seeding conference champions higher. I would have gone even further and seeded the fifth conference champion fifth. That makes it "qualifiers" and "second chance" teams. Texas didn't "deserve" a spot in the playoffs. They were granted a second chance by the committee. The ACC champion didn't do well this year. If the Big12 and MW champions don't do well either, then it will prove that the Big10 and SEC teams were better. If Boise State ends up winning the championship, then all of the people who have been saying for 15 years that they haven't deserved a chance will be proven wrong.
"Best" teams is entirely subjective, and is driven mostly by companies that want you to watch TV, or want you to place online bets. I remember one commentator who said one year in the 2000s that Boise State didn't deserve to be in the BCS game until they proved for several years that they were that good. Then a few years later, the same commentator said that Boise State didn't deserve to be in the playoff, because they should have proven their case even more the first year and now they were old news. It is all entirely subjective, and the important measurements change to match the desired outcome every single year. Are "big wins" important, or are "bad losses" detrimental? Well, one year it is "obvious" one way and the next year it is "obvious" the other way. Make it ALL qualifiers. Have all 9 or 10 FBS champions be "qualifiers", then have a smaller group of "second chance" teams. Then it will be a real championship. Now it is still a pageant. Better than before, but still largely based on the perception driven by companies with financial interets.