Does this setting affect the game?
Spoiler
(http://i.imgur.com/Xy9Byqo.gif)
No, it's just for preview purposes. In-game, character animations are centered (so if two frames are not the same width, they'll be aligned according to their "center pivot" and bottom edge), while button and object animations are aligned according to their left edge (and the top edge for buttons, bottom edge for objects, I think).