Kuro the Artist bought a lot of early scripts and documentation for the movie that were from someone who worked on it and were sold on E-bay, and did both a video and a live reading of them, and each one of them explained Eon in some different way, but mostly doubling down on the idea that Eon is an omnitrix construct that takes over Ben's body and is in a perpetual cycle until he finally can use it to open the Hands of Armageddon.
So basically the idea was mostly that Eon was always intended to be Ben, or at least, Ben's chronian transformation that is trying to be set free from the omnitrix, although the exact reasoning and method changed depending on the script. The final version kinda of still implies that, but early versions were much more clear and had a lot of plot points that although not used in the movie, still were referenced in a way or another that shows how all over the place the production as and they were working from multiple scripts back to back.