It would seem the creaters had Kefka destroy most of the world after the floating continent so that it would be somewhat symbolic of what happened at the end of the War of the Magi. The world was destroyed back then so the goddesses became statues. When the goddesses come back to life the world is brought to a state of destruction once again. Also, magic is far more prevelant as a monster's attack in the WOR, saying that once again magic is a natural part of the world.