There's no disadvantage to that method as far as I can see.
That was how I started out doing things, because it is so neat. But I think there are some disadvantages:
1) Quest fragment scripts are the least readable scripts in the game. Particularly because fragment numbers aren't obviously related to stage numbers. Of course comments help here.
2) Quest stages occasionally become associated with the wrong fragment number, causing much mystification and gnashing of teeth.
3) As AmethystDeceiver has noted, dialogue TIFs can be changed or deleted without problems, but deleting other scripts (or their properties) causes Papyrus to complain in perpetuity. Making TIFs perhaps the best scripts to use whenever possible, despite their horridly unhelpful and unprefixed names?
4) This is speculative, but it seems to me that having a larger number of smaller scripts could help the game take advantage of multithreading, when that's desirable. I don't suppose this matters when all you're doing is setting objectives, but it might count against doing everything in a quest script.