I know that the design of the Legacy Chocobo comes primarily from the Yoshitaka Amano art, but I was wondering just exactly what happened to our feathery companions from 1.0 and how they came to look as they do now. Is there any official lore on what happened to them?

Reading the official in-game description of the mount:

"Five years and a realm-shaking calamity were not enough to break the bonds between you and your loyal steed. A single whistle and he will be at your side once again."

Which sounds to me like the bird remained behind while legacy players were sent forward. I think this is supported by the longer plumage, and that the bird is wearing strange gear. But the bird also has the brand of the Twelve on the beak, which was only supposed to be on those sent forward in time (if I understand it correctly).

So... is there any official word on what happened with the chocobos? And, if the bird stayed behind for five years, how did it get the brand/armor?