The rules about advancing muffed punts and non muffs after the kicking team has touched the punt don’t make any sense to me.
Once upon a time the defense wasn't allowed to advance fumbles either. The rule was changed specifically so that a fumble could be advanced.
However a muffed kick isn't a fumble, it's just a kick. Normally it's illegal for the kicking team to touch a kicked ball (the "penalty" for which is that is belongs to the receiving team at the spot of the touching). However it's no longer a violation if touched by the receiving team, which is why the kicking team gets to maintain possession. The ball is dead because it doesn't make sense to keep the ball alive when 99.9% of the time a kicking team touching the kick is going to mean the ball belongs to the receiving team, so there is no point in continuing the action.
You might say, "why not just kill the play only if the ball hasn't been touched by team B"? And I would say that 1) it would create some really screwed up penalty scenarios. 2) It would be a case of a ball becoming dead only if a team has committed an infraction, whereas in football typically infractions are dealt with after the play and have no bearing on how the play itself ends up (we don't kill a play after throwing a foul for holding, for example).
EDIT: Definitions are important in football. There are three "loose ball" situations that casual fans / announcers treat as the same, even though they can have dramatically different results in a game. Those are:
1) Fumbles
2) Loose kicks touched by B
3) Backward passes that have been muffed