Do note that the change was also made to increase the over pacing of the game when entering a dungeon and applying buffs. I remember how we would sometimes spend minutes just getting everyone buffed before pulling any type of mob, I think this change was done to decrease those down times.

It may seem like a very small thing for most players but as a healer who sometimes has to run after players just to give them 2 buffs, I would rather not do so for 3.

Edit: Also, this change is mostly a "continuity" difference from 1.0 and other FF games rather than a "lore issue" as this does not really change the story background of the world or any character.