Hey, so I have actually thought about this a little bit, even though I haven’t written any sci-fi.
Besides magic and the breadth of understanding, I feel the primary distinction between most sci-fi and fantasy, at its core, is exploring the differences and similarities between us and literal aliens. With that in mind, I think the place to start is to start with God’s character and creativity. In sci-fi, it is very common for aliens to have completely exotic forms of social structure or reproduction, for example. But these things all derive their inspiration from strange and wild things God created actually here on earth. While God created us very specifically and purposely, He also relates to us to where we are at. I think the special thing about sci-fi is it opens up the possibility to ask questions like: ‘how would God relate to a species with a literal hivemind or asexual reproduction? How would they view Him? If they are fallen, how would their fall be different from our own? If they aren’t fallen, how would they relate to us or how would God use them in relation to us?’.
I feel like this method gives you starting place to create species who’s religion looks and sounds as alien as they are, but is fundamentally based upon the same creator, preserving both God’s character and the sci-fi aesthetic. I would caution that it is easy to be drawn into weirdness when doing this, but at the end of the day, you can always pray and ask the big man himself 🙂