We as the player know only as much as the main characters know, and they're in the dark about a lot of things even up until the end of the game.

I reckon that most of the facts we've been told are lies or distortions of the truth. There are far more pieces to this puzzle! The fact that they were able to loose their brands after explicitly being told that they will become a Crystal or a Cie'th tells us that the 'laws' aren't as set in stone as we think they are.

I think we'll learn more about the mythos in the other FNC games that may shed light on these 'inconsistencies'.