This is a great way to think about it, and any belief system that you don't question sounds like it might not be good enough or if you can't question sounds pretty suspicious.
I had to go to a Christian church a lot as a kid. My parents are believers and met at church themselves. I have always thought it was nonsense from a very young age because I felt the stories had too many holes and too little evidence. To your point, my love of science fiction and fantasy as a kid really showed me how much better some of the 'origin stories' for worlds could be if they were organised by a decent writer.
What really fascinates me are the fervent believers who come up with their own fantasy worlds. CS Lewis or Brandon Sanderson are easy examples. But that's a discussion for another day!
I agree with the Witcher and American Gods, I'd also suggest many of the works of Arthur C. Clarke and echo Hitchhiker's Guide by Douglas Adams. They've both written some excellent things about science fiction and religiosity.
Great post. Thanks for sharing!