Chocobos are in a weird place in the game's system. They are pets, but they count as players in the party list. I'm guessing they haven't found a way to not break this while transitioning them to pets (or something similar) that can be summoned inside the dungeon. Then again, that could just be bunk and they don't see it as a relevant priority. Who knows? It was mentioned in a recent live letter and was mostly made fun of for being brought up too much.