It's inherent to a sport that allows 64 teams in the field, which has been the case for a good while now.
The rest of it is just the nature of playoffs, which are built to reward the hottest team at the end, not the best team over the course of a season. It doesn't usually come up in such a glaring way, because generally the best teams throughout the season will emerge as the hottest teams at the end. But the possibility is always there, and it happens.
I don't think anyone should argue for the Sooners as the best team throughout the season, but it's hard to make a case against them being the best by the end of it.
Just depends on what type of champion people want. This sport picked the Best-At-The-End model, but at least the Sooners will have dominated their way through some good teams in their own backyards. Whatever negatives we might say about the Sooners' regular season, Omaha is built not to be reached by a team who didn't earn something.