Windaria/WMG

Windaria is actually Sol Ciel
There's a large floating metal construct high above the sky, presumably too high for any airship to reach. It could be one of the three towers. Secondly, when people die their souls turn into birds of red light and these same birds feeature prominently in the opening scene of Ar tonelico II: Melody of Metafalica. The guess is thus: the actions of Alan and the Shadow Lands damage the planet's Heart of Gaea and a program was thus created to ensure that everyone was evacuated to one of the towers.