A bracket will probably be held up by two players playing the full 3 games, so I don't expect two players playing a 10km and 20km will delay a tournament. Let's also not forget the not-so-rare occurence of players having draws on 5km maps, meaning they need to replay -> more time needed.
Also, let's use two hypothetical equally skilled players, although ones strongest suit is 5km, 2nd 10km, 3rd 20km, while the other is best at 20km, 2nd 10km, 3rd 5km. How exactly does the first player not have an advantage here? He has a high chance of winning the first game and a ~50% chance of winning the 2nd game. If the small map player wins the 2nd game, the big map player won't have a chance to play to his own strengths
Having no 5km maps in the loser's bracket does benefit players who are better at large maps, though, yes