The advanced stats (i.e. kenpom) don't measure who is the best, they measure who is the most efficient. And they use a definition of "efficient" that was created by the stats guy.
Using them as a strict ranking of who is "better" is not using the stat the way it is meant to be used.
Using a committee allows various definitions of "best" to be considered.
Also, being ranked 50th would generally not get a team in, there aren't that many at-large spots.
How could a team be more efficient but not as good as a less efficient team? If you score more pts per possession and give up fewer points per possession, weighted with SOS, then aren’t you the better team?