i donot see a disadvantage in any of these aspects? My English is not very good, so bare with me please:
Ratings go up and down all the time. Many have higher ratings for a while because they won by timeouts; but they will loose those points the more they play, as they don't have the abilities to defend their rating.
Moving on "undeserving" to the next round will auto-correct itself, as long as there are others around still playing. We loose against stronger players, regardless of what the ratings show. In the end, it's one's abilities that wins him the tournament.
If everybody but one has left without playing the next round = Is Equal To = nobody's around who can beat him. In which extreme case he deserves to be the winner anyway.
Yes faster rounds in tournaments due to people resigning is not a disadvantage, it just shortens the process.
People usually resign because they realized they have no chance. Their resigning doesn't really change the outcome?