This is the most often I've read someone talk of "God" or the bible in an assertive stance in many months and it's from a self-proclaimed atheist no less. 😵💫
I wonder, if the Wired editors made him change it, so that no religious people would be offended...
Oh yeah, I have no problem with using a metaphor, whether it's from a religious book or not. It just weirds me out how it is told as if it's a historical record with no doubt of it having happened that way.
For an atheist, the stories in religious books are more like fables – you don't believe that it happened that way, but you can still draw a learning from it. And when talking of fables, you don't recount them as facts, rather you point out every few sentences that you're simply recounting what's being told in the book.
You can do that in a neutral way, too, where you just say "the Bible reads..." and then people can choose to believe in it or not. And this text rarely does that, while also throwing in some opposite tropes. Had the author not stated that they're an atheist, I would have assumed they're basically a religious fundamentalist.