In-game, Phoenix uses the "01 [Default]" palette (as to be expected) for her boss battle's opening cutscene, then switches to the "Dark Phoenix" sprite set after her transformation animation plays out. However, it seems that her boss sprites were based on an earlier version of her palette -- the same one seen in the "00 [Placeholder]" set, judging by how her hair and yellow accents appear brighter in comparison to the final palette used in-game. This sprite set makes her palette match the intro animation's from her default palette's sprite set.