Nope, that's the way the playoffs works, in all sports.
Does the Superbowl have a credibility problem? Do the NBA finals have a credibility problem? Does the Stanley Cup have a credibility problem?
At the end of the day the champion is the one holding the trophy. Nobody questions that, if you want to have a private celebration for the team that won the most games have fun. It'll be a lonely celebration.
Besides, the point of sports ultimately is entertainment. Nobody really cares if the team with the most wins in the regular season wins the championship. Every team enters the season knowing full well that the winner of the playoffs is the champion.