Zodiark was effectively imprisoned until Fandaniel and Zenos broke him out, yes. Even with that, he was basically bereft of a heart, which is why Fandaniel could pilot him. Elidibus was Zodiark's heart, he was Zodiark. What was left after his "death" was basically just a half-mangled meat mech. And yeah, he was kept around for the sole purposes of maintaining the aetheric barrier (while in stasis) that kept the Final Days at bay.