For major conferences, conference tourneys are about money and nothing else (except perhaps sneaking another conference team into the tourney, though that will often put another conference team at risk of falling out). For mid-majors and below, they're about making the tourney.
Regular season championships are what any sensible fan cares about (and yes, I'm aware that OU doesn't have many of those, either) because they are earned over the course of eight or nine weeks of consistently good play. Conference tourneys can be won by a so-so team on three-day hot streak.
That's ridiculous, and you don't translate the same logic to the national championship. The NCAA Tournament does not always crown the best team for the exact reasons you stated, yet, winning is the pinnacle of achievement. You are considered the NATIONAL CHAMPION whether you were the best team that year or not.
Regular season games are also impacted by a number of variables that sway who the best team is... such as home courts, luck in scheduling, home cooking from officials, random explosions by crap teams on their home court, etc.
Having the best regular season record is a great thing.... But to crown someone a champion based on that record isn't done ANYWHERE, in ANY sport.
The best regular season record in the NBA wins you nothing.
The best regular season record in the NFL wins you nothing.
The best regular season record in college basketball wins you nothing.
The best regular season record in the NHL, MLB, MLS, etc win you nothing.
In the NBA, you have to win the playoffs. In the NFL, same thing. To win the college football championship, you have to win the national championship game in a playoff. Etc.
Only in this ONE instance are fans, for whatever reason, trying to assign a championship to someone based on their overall record. It's completely absurd and without equal.
I originally thought it was something the Kansas' of the world cooked up to reward themselves for when they didn't win the tournament.