I know. I am making an analogy. I realize that it involves some reasoning, but try and follow:
Conference play results in standings. Whoever is atop the standings and the end of the regular season is the regular season champion, which you believe is the true measure of who is the "best" team, even if that team does not win the conference championship.
There are also National rankings, and at the end of the regular season the team atop those rankings is awarded the top seed in the NCAA tournament. By your logic, it would seem that you believed that Duke, which finished the regular 1998-99 season atop the rankings and was awarded the top seed in the NCAA tournament, was the "best" team in the country that season, even though they didn't win the National Championship.
Capisce?