Do realize that the author is Czech. While being religious is the default and atheists face (mild) discrimination in places like the US, at least until the 1990s and the fall of Communism, things were reversed in (then) Czechoslovakia, with state supported atheism and religious people viewed as suspected dissidents.
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It feels different if someone has recently been discriminated against. Jokes land differently when they are too similar to reality.
That said, making edgy joking is definitely acceptable, you'll just alienate part of your audience. That's why the hollow corporate bs doesn't do it.
Do realize that the author is Czech. While being religious is the default and atheists face (mild) discrimination in places like the US, at least until the 1990s and the fall of Communism, things were reversed in (then) Czechoslovakia, with state supported atheism and religious people viewed as suspected dissidents.