The devil's advocate response to your 'bad part' scenario is that only one team can advance from the Region The two best teams are likely going to end up playing each other at some point -- what difference does it make if it's the first game or the third or fourth game. That said, I agree with your comment. In a perfect world, the two best teams would play in the Regional championship game, not in the opening playoff game.
You want a bad scenario: take one of those winless teams that S1nglewing is talking about. Let's say they avoid a play-in game. Then, the team that they are scheduled to play in the first round gets hit hard with Covid -- so hard that they are forced to cancel their game, resulting in a forfeit. And then, low and behold, it happens a second or perhaps even a third time . . . next thing you know, you've got a winless team winning a regional championship. Talk about an asterisk! I mean, something like that could only happen in 2020.