Man made race.

[Kotemon]

Some Gigas in Mor Dhona claim they are descended from the Allagans (leves). Other Gigas were shown to believe the Crystal Tower is a holy relic of sorts in their lore. Then there is still no back story to why Gigas began appearing out of the ground in Copperbell mines. Asside from saying they are now free from their masters. Lalafell? Then that ruined door in the boss room seems to be part of a structure separate from the mine.

Then there was the appearance of Mamool Ja in the Crystal tower and World of Darkness for some odd reason. The dragons in CT were probably mindless engineered stock from Azyzla long after Mercydia fell.