You do not have to be the best team in the league to win a knockout competition. As any sport with a playoff-structured postseason knows, the most dominant regular-season team, and statistically thereby the best team in the league, does not always win the playoffs.
In global football, the most comparable situation is perhaps a domestic, straight-knockout cup or an international competition. Portugal won the 2016 European Championships by winning just one game in 90 minutes. They were not the best team in the competition, but they found a way to win it nonetheless.
The Portland Timbers very nearly did the same last season.