Keep this in mind- FATE was able, through great effort, to bind Miguel as the DS's Guardian. This means she does have a certain amount of control over Home World, but compared to her control over Another World it's nothing.
FATE could have used the FATE distortions, bypassing the Dragons' seal, to simply send waves of destruction to another world. The three islands could then direct at the Tower. FATE calculated what would happan if Serge dies, i.e. the split, and made sure that she could destroy the sea when the time comes.
Also, keep in mind that 2,400 A.D. could have been rounded down to 2,400. It could 2,436. They would create a company called 'COMPANY 2400', the same way companies called themselves '____ 2000' during the end of the 20th century in our world, yes?