The Tree of Life in Evangelion
As far as Evangelion goes, there's several statements from the staff concerning their placement and usage within the show (emphasis is mine):
From the Hiroyuki Yamaga: May 1998 issue of &quot;Evangelion&quot;:

On the reasons for use of Judeo-Christian symbology in Eva
YAMAGA: I don’t know exactly why. I suspect that Mr. Anno may have read some book on it, and there was some thoughts he wanted to express on it. I personally am glad that, rather than Christianity, he didn’t express some obscure Buddhist theme, because then it would have been linked more with Aum Shinri Kyo. [LAUGHS]

From the Kazuya Tsurumaki: Q&amp;A from &quot;Amusing Himself to Death&quot;:

Can you explain the symbolism of the cross in Evangelion?
Kazuya 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.

And from an NHK special &quot;Extra Curricular Lesson with Hideaki Anno&quot;, a student asks:

&quot;Why is that robot-looking thing called an Evangelion&quot;?
Anno: &quot;It is a Christian word meaning Fukuin or Gospel and it's supposed to bring blessings. Actually, it's a Greek word. I used it because it sounds complicated&quot;

So in the case of Evangelion, it's used mostly to look cool. It's
more or less an internally consistent window dressing that doesn't contain any actual religious meaning. That is not to say that the symbology doesn't have other meaning within itself, especially in the context of the fictional show.