the solution to the three 5-4 vs one 9-0 with one 8-1 being left out is to add a "semi-champ" week that is flexible.
Split the conference into east and west, then split those divisions up into pods. Top two in a division, regardless of pod, play for the spot in the conference championship, while the other 6 teams get a flex scheduled game with whoever is left, which would presumably play into New Years Six or whatever contention if they're good enough.
That way everyone gets same number of games minus conference championship game, but one of the games is used to settle division disputes. If there is a team that is 7-2 with both losses coming to the 9-0, well they had *two* chances and blew it, argument over. Pod "champion" is essentially meaningless, but who cares if you're the champion of a 4-team pod? Pods only exist to make full 16-team scheduling logical over the course of many years, not really to decide the conference champion.