Upon review, it seems that the Gamecube primarily stores data using big-endian (a type of data encoding), whereas the PS2 primarily stores data as little-endian.
This means that some game data (e.g. dialogue files) might appear to have their data “flipped” when comparing the GCN and PS2 versions.
As an example, a section of data might be “cdc3b0b0” for a file in the PS2 version, but “b0b0c3cd” in the GCN version.
This means that certain files were re-encoded when the game was ported to the PS2 to avoid them from being read as corrupt.
Shoutout to Dahni in the Discord chat for making this discovery.
It’s unclear at this time exactly which files were re-encoded. It seems that dialogue files were altered at the very least, but this could extend to other file types (textures, models, etc).
With that said, I’ll be focusing exclusively on the GCN versions of the game files to prevent any confusion of endian encoding going forward.