I see 2 obvious interpretations. The scientific one and the religious one. I think the first one makes more sense and more elements point in this direction. For example the main character, who is an embodiment of science. Also his dad is an embodiment of mathematics.
I really don't think the religious one makes sense in context. There are too many elements pointing away of it. Although it might be something like "god is actually just yet another being, but a more advanced one", but it would still be within the scientific interpretation. But I don't think it's about gods/kami, unless one can find a specific kami which matches her. It might be a first contact story as well. I actually don't have my own hypothesis who she was. I think there were not enough data. Have you seen Kaido? She might have been someone like that. What are your thoughts?