That's the problem with new writers and retconning....what is said and done in one book is changed or tweaked in the future. Happens to almost every character at some point. Fact is that Nate is not an omega per Hickman, and he's not even in this reality currently as he's quasi-dying from overusing his power and the Life Seed. Maybe he'll come back and they will explain how/why. But he's off the table as of now.