His hypothetical is “suppose atheism doesn’t win”. His conclusion is not “then atheism doesn’t win”, so he’s not writing his hypothesis into his conclusion. Rather, his conclusion is “then rationality doesn’t mean what one of your other premises says it means”. That is not saying P and concluding P; it is saying P and concluding something logically equivalent to P.
His hypothetical is “suppose atheism doesn’t win”. His conclusion is not “then atheism doesn’t win”, so he’s not writing his hypothesis into his conclusion. Rather, his conclusion is “then rationality doesn’t mean what one of your other premises says it means”. That is not saying P and concluding P; it is saying P and concluding something logically equivalent to P.