So my Wind-up Bahamut code has already been used...?

[Eekiki]

Probably due to the format. This isn't a CD album it's a Blu-Ray. They probably elected not to compress the tracks for digital distribution.

Except the blu-ray includes MP3s of all the songs, so there.

the only exception is the "secret" Gilgamesh battle theme

I can't read Japanese. How do you unlock that?