So you’re uncomfortable comparing teams from different conferences because they played different opponents.  But you’re comfortable comparing teams from the same conference despite the fact that they, too, face substantially different opponents?

And all of that aside, let’s say that a wild-card team upsets their division champion.  Well, so what?  Isn’t the wild-card team deserving?  If not, why not?  If all you cared about was the sanctity of some regular-season record, of who "deserved" to win, then why bother having a championship at all?  Add 3 games to the regular season and declare the winner by their W/L record.

but if each team plays each other team only once, then your n for any given matchup, which seems to be the critical point here, still equals 1.  For example, consider two teams A and B, each with an 11-1 record, but team A had beaten team B, and team A’s loss had come from a team B had not faced.  In a wild-card situation, perhaps both teams A and B would be in the playoffs.  In your situation, the fact that A had beaten B would disqualify B from the playoffs based on a single observation.

in what way is the regular season a better arbiter than a championship game?  it sounds like sour grapes, to me.  after all, most college teams in the same conference meet each other only once, if at all.  you simply can’t draw parallels to baseball in that regard.