I do remember that Krelian starts talking about Mother God rather late in the proceedings.
Yeah, and this prompts the weird bit from Citan about "Mother and "Great Mother" and Deus wanting to slurp everybody back into her womb whether they're fated or not. They make a big deal of it at the time, then never mention it again. Oh, Disc 2, you little scamp.
I don't remember if other people call Deus Mother God, either, so when my memory of it iced over, it did so with a pretty genderless outlook in regards to Deus.
Very early on, there's Grahf's "haha naru kami", or "Mother God", which is referring to the one he plans on destroying, and hence to Deus. There are numerous references beyond that point, some of them unclear in precisely who they're referring to. I will have to commence work on a comprehensive list!
I'm sure a genderless outlook was facilitated by Honeywood's choice to nearly always omit pronouns when deities are being discussed. (He did slip up in one place I recall and call W.E. "he", which doesn't quite pan out because the only gendered human characteristics the W.E. has at all are feminine ones, as it says to Fei's metaphysical face, but anyway.) This isn't an invalid
choice, and was probably even wise given the climate of the times. Opposition to Xenogears' localization wouldn't have taken well to God being characterized in the feminine, I'm sure.
But in an ideal translation, I don't think "it" works very well, for the reasons I provided previously. It is expecting an unnatural level of detachment from the characters who live and breathe that universe. If they talked about God using a neutral word like "creator", "progenitor", or "parent", then "it" might work, but humans usually aren't comfortable with that kind of ambiguity. They want a big mom and/or dad up in the sky watching over them, and their language will reflect that.
(That said, there is
some research on Japanese pronoun use with regard to deities that I need to do, in case I am needlessly making myself sound foolish...)
Looking at concept art of the Deus boss, it seems very feminine as well.
Speaking of which, it took me stupidly long to realize that Final Deus incorporates a lot of Opiomorph's design. I wonder if that's meant to signify anything "deeper"?