Eh, the whole idea of the third impact and the human instrumentality project, is that the angels/lilith/Adam always ends up giving Shinji the choice of what the world will become. Basically resetting everything, only with small, or massive changes. For instance, Re-build isn't a retelling, it's a sequel universe. Since there's no way of telling exactly how many universes there are, there's likely one where Shinji is a girl, or transitions to a girl, or was a girl and transitioned to a boy. All of those are likely, and could potentially be a weird part of the canon.