No. It happened because teams that win their division automatically make the playoffs. Which means that clearly better teams sometimes don't make the playoffs at all. There is no committee to step in and ensure that the best teams make the playoffs. When a 7-9 Washington makes the playoffs it's an embarrassment to the NFC Central Division, but we move on with our lives.
At the moment, the NCAA has a committee entrusted to putting the four best teams in a two round playoff. Given the imperfections built into the system, they've done a pretty good job, and nothing remotely close to putting a .500 team in over an 11-5 team, so I'm not sure why you introduced that question.
The National Championship is a lot less mythical than it was when Bowl Games called the shots and two different polls often crowned two different winners using highly emotional criteria. It will end a lot of arguments when the playoffs get expanded to 8 teams, except for fans of the #9 through #16 teams.