Great news, I figured out a foolproof way to avoid the 3 Unbeaten Team possiblity!
Caveats:
No ties allowed
Number of Conference Games is at least equal to the amount of Teams in Conference divided by 2, less 1 . For example, if the Conference has 20 teams need at least a conference slate of 9 games.
Any given year split the teams in half, does not matter how including based on geography. Could be, East-West (naturally this would protect rivalries the best), North-South, previous standings, alphabetical, random draw... whatever.
Ensure each team in the group plays round robin, voila no more than 2 teams would be undefeated. If schedule allows for crossover games, so be it, but in the end there would be no more than 2 teams without a loss in the Overall Standings.
In simplified terms, the exact same current scheduling rules could exist without change and no more than 2 teams would emerge unbeaten.
Way too much time on my hands? Obsessive compulsive? Guilty as charged, but the conundrum was bugging me.
Imagine no Divisions, it's easy if you try.