There's a gaping hole in your logic. With empty space, we can compare it to "non-empty space": We can see how photons, atoms or subatomic particles react in an environment of "empty space" and an environment containing matter. Therefore we can obtain actual data, and look at the differences between the two environments.
You simply don't understand what you are talking about. "Photons, atoms or subatomic particles"
are an environment of matter as well as energy. No matter contains matter within the essence of itself. All matter shares empty space. Empty space contains matter. You really need to brush up on your basic science.
With a god, such a comparison is logically impossible. We can't compare an environment with, or without a god, because only one scenario is logically possible.
An atom resides within empty space. There is empty space within the atom, between the electrons, and between the electrons and the nucleus. Empty space is within, without, and "flowing" through all material and energy.
The only difference with God is, He even made the empty space. So, we absolutely can use the relationships between photons, atoms or subatomic particles in empty space to prove that God exists.
Therefore, scientific proof of a god cannot be compared to evidence, or proof, of "empty space".
Your move...
Therefore, scientific proof for God absolutely can be compared to evidence, or proof, for "empty space".