I think there is a quite important subtlety here that you may be glossing over. We should not confuse how science enquires about the natural world, which is as you say, with what scientists necessarily think about God. Not all scientists, by any means, are philosophical materialists. Many are religious believers. They approach the study of the natural, physical world according to the scientific method, because that is the best technique for that task, but not to the exclusion of the presence in their lives of a non-physical, aesthetic and spiritual dimension.