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There is a lot of thought into how he could be so powerful than there is cold hard evidence of it. Probability over possibility for sure, but nothing concrete. What we do know with 100% certainty is that Zenos is augmented. We know that Garleans do not possess the ability to manipulate aether in the form of magic, and have had to rely on technological development in the form of Magitek. We know that these advancements were so profound that they could battle with the likes of Midgarsormr. Even though he was much weaker than when he resided on Dragonstar, this remains an exceptional feat for the Garleans. I think you can see where I am going with this in regards to Zenos' augmentation.
As for Zenos' visions of the Final Days. I think that just lets us know that this cataclysmic event left its mark permanently on Zenos' soul. He is after all, sundered just like everything else. Amon spoke of always being haunted by the memories Hermes attempted to cast into the void. This is only speculation, but perhaps Zenos possesses a sundered soul from one of the other members of the convocation. I would need to look at the purpose/duty each one had again, and see if any of them relate to Zenos and his behaviour.
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I doubt he contains a soul from one of the 14 from the Final Days. Emet would have recognized him as well as possible Hythlodeaus when we were talking to him on the moon. He recognized Fandaniel but never once recognized Zenos and both he and Emet can see the color of souls.
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Lahabrea could have told us Zodiark and Hydaelyn were primals back in ARR. They could always easily write in why Zenos' soul has not been recognized, so long as it serves the plot they are trying to progress. I'm not saying this is definitely the case. Just tossing out some passing thoughts.