In your hypothetical, the Indians have won their division but are the fourth seed and have to play an extra series, right? If the Indians have won that division despite strong competition from good Twins, Tigers and White Sox teams, they might be the best team in the league.
No, not with unbalanced schedules. If you have three strong teams in one division, they all have to play each other 18 times over the season, and will presumably each lose a bunch of these games even though they’re playing relatively well. A less-strong team on its own in a weak division only plays those good teams six times each, while they get 18 against each of several bad teams, and the opportunity to run up their record.
Look, I’m not saying that teams with better records across divisions don’t tend to be better. I’m saying that a difference of a few games one way or the other between teams that haven’t played the same schedule isn’t proof, and shouldn’t be the basis for such a huge structural difference as having to play an additional series to advance or not. A three-game margin within a division is more telling than a six-game margin in different divisions.