Correct headline is that the current Batman writer wants to write a story about an atheist Batman.
The Batman of every version of the DC Universe I know of personally knows multiple aliens (starting with Superman), multiple magic users starting with Zatara and Zatanna, and including The Spectre who is the personification of Old Testament style divine retribution.
Theology aside, atheism would not be rational for a person with The Batman’s life experiences.
Nearly all of the current comic book writers see themselves as social justice warriors.