Eagon is actually Valdo Caeserius
Think about it: Zana feels like she failed her father, and the best way she can do that is by giving him a better chance at life, free from the Templars.
What if she used the Atlas' abilities to make a copy of him when he was young, and moved that memory into reality. She sponsored the family raising him and made boundaries to make sure he doesn't know of his Caeserius lineage. Even the maids lines "Valdo's favorites" could mean "Eagon's favorites" and her babbling caused her to disappear. To keep him away from the Atlas.
Even the environmental lore fits: https://www.poewiki.net/wiki/Aberration
Zana feels foolish about underestimating him, that she knows he could take up this path, and would do so without her blocking him.
Eagon himself feels like he's at least as good as his father, he feels attracted to the Atlas, and his potential. He doesn't feel an attachment to his father, just jealously? envy? competition? Meanwhile he loves Zana deeply, for no explicable reason. Why the difference if both are family? (Although it might stem from just the abandonment part)
It explains why Eagon is so out of place, why he has such a strong grip on memories & the atlas despite being disconnected from it for so long, and why he cares so much for Zana and saving her. Valdo himself never once mentions Eagon, just Zana & his wife, because he never knew Eagon, he is Eagon.