The reason Eva has relgious refrences
at the Otakon anime convention held in 2001, assistant director Kazuya Tsurumaki (who was the director of The End of Evangelion: Episode 25' Air - while Anno personally undetook The End of Evangelion: Episode 26' Sincerely Yours and acted as Chief Director) was asked directly what relvance Christianity had to Evangelion. This was his reply:
Tsurumaki: There are a lot of giant robot shows in Japan, and we did want our story to have a religious theme to help distinguish us.
Because Christianity is an uncommon religion in Japan we thought it would be mysterious. None of the staff who worked on Eva are Christians.
There is no actual Christian meaning to the show, we just thought the visual symbols of Christianity look cool. If we had known the show would get
distributed in the US and Europe we might have rethought that choice.
Tsurumaki also directed or helped directed several episodes of the TV series and worked on storyboards, as well as being credited as the assistant director or the TV series.
so that's the deal