>>714574075That theory is correct. The game literally states Ark and everyone else are duplicates created from crystal who, at the end of the game, are 'returned to true form' by Dark Gaia.
Post Dark Gaia's defeat, Light Gaia cannot sustain the spell because it cannot affect the underworld's crystals. It can keep it going for just a bit longer, like a terminal patient on life-support, but it cannot fix it being undone.
That's why eventually Ark is scooped up and his soul reimplanted into a bird by Light Gaia. He gets his true final wish, in the moment's of his final death: to see the world, the whole world, that he fought for flourish.