Also do not forget that Hydaelyn Herself actually hinted that Zodiark is already existing somewhere in another realm (the Void?) - She states this in the cutscene after
freeing Thancred from Lahabrea's control:

Originally Posted by
main scenario quest 'The Ultimate Weapon'
Hydaelyn: "Hear. Feel. Think."
Hydaelyn: "Warrior of Light. Beloved <son/daughter>."
Hydaelyn: "The Darkness hath fled before the unclosed brilliance of thy spirit."
Hydaelyn: "Yet it lingereth still beyond the sight of men, in forgotten corners of the world."
Hydaelyn: "In the depths of the abyss yet resideth the Dark One, watchful ever."
Hydaelyn: "Till this evil be cast out, never shall the world know aught but a passing peace."
Specifically, Hydaelyn's comment definitely seems to suggest a doggered duality between the two, which would also make Eldibus's statement about "balance needing to be restored" actually strike true (and also contradicting the other Ascians previous comments about bringing about Zodiark's "rebirth").
But either way, as Moose said, Zodiark's true identity is a big blank at this stage - is it that 'dark Hydaelyn/Mothercrystal' seen through the Echo at the very end of the 2.0 ending scene, is it that weird, vaguely humanoid crystalline statue... thing... Nabrieles strung Minfilia up in front of in the Chrysalis, or, paraphrasing what my Path Companion said way back in 1.0, "is it something else? Something we are yet to see? Something, more?"