If you try and choose the four best teams, period, there should be zero extra emphasis on winning your conference. It should not be a factor beyond that you beat an ostensibly good opponent. A team that looks mediocre early perhaps due to injuries and looks like 1995 Nebraska the rest of the season should be considered strongly even if they are 9-3. Best team should need no qualification.
The committe changes up fairly often in personnel, so it's not surprising they collectively weight different factors differently. I think they do a decent job, that fourth slot will always be contentious.