Well, in 20CB there was that one part
[SPOILER]during the priest guy's flashback when the future pope guy gave him a bible and asked him to see if it was real or fake. When he gives the book back, he says that it's fake but what was inside it was real.[/SPOILER]
But other than that, what you said was pretty much what I meant.
Though I haven't read it yet, Shelter of Wings is a Christian manga that looks pretty interesting. Also, check out Manga Messiah.