The story would be no different if the scientist was talking to a priest, and neither would its message be. The point is that for logical arguments, about matter or philosophical, you must always start with some set of a priori content to work off of – axioms in logic and the universe in physics. Any physical process by definition can only work when given a universe to work in, you can't possibly derive the universe from nothing because all scientific models by definition describe how the world evolves, and a lack of the world can't.
A naïve person would then argue that hydrogen must have been created by their God, that the existence of the universe must be the doing of their God and that proves that their God must exist. A scientist would interject, as that's a whole load of assumptions which are untestable and the simpler theory, that the universe just exists as an assumption in itself, is a much better one. A less religious person, however, would argue that God is that abstract fact of pre-existence, a pre-existence that all the scientific investigation in the world could never get rid of.
All philosophy of science starts with the set of assumptions known as materialism: the world exists objectively, and its phenomena can be measured and explained. We can't possibly ever escape the assumption that the world exists with any scientific theory and therefore must accept some kind of pre-existence.
The argument does not actually support the existence of a conscious, material God any more than just saying that you believe in him. It simply argues that science can never explain the existence of the universe, just its development. Intelligent design is pretty much excluded.