Because the late-game is incredibly easier if you avoid leveling up in the early-game. Or worse, if you level up mid/late-game with bad equipment, your stats will suck. This mean that every time you level you have to make sure you have the right items equipped. This doesn't really matter in vanilla but it creates a lot of variance in higher difficulty settings.
Also on topic of buffs duration, it's indeed annoying but unless you force Active ATB it's a necessary evil. If you just buff the duration, you can still artificially increase it even more by going in the menus with the Wait ATB option.