In the philosophy of science, evidence and proof is based on that which we can all agree upon using our sensory systems, and then independently reproduced in the lab. This method factors out subjectivity. Although this philosophy is useful for differentiating physical reality, there are nevertheless aspects of reality that are real which are ignored by this standard.
For example, say I had a dream. I carefully relate the details of my dream. This would not be called evidence or proof of this particular dream, even I was 100% objective and accurate. The reason is, even if I was being objective to what I saw, others cannot directly see my dream to verify the details, nor can this particular dream be reproduced in the lab. Yet, science knows we dream and everyone has had a dream to know that dreams are real. Dreams detail is just outside the philosophy of science. Religious experiences tend to overlap this unique area of realty, that is just outside the philosophy of science.
The philosophy of science was originally designed to factor this area of inner reality, so science could specialize, and deal only with external sensory reality. Atheism has misinterpreted this specialization of science and assumed that if science does not make provisions for certain things, it does not exist. Science was not designed to deal with certain types of phenomena, and therefore has little to say in terms of things outside its own standards.
It is possible to bridge the gap, but this requires a revised version of the philosophy of science, that would allow science to better deal with this final frontier. This final frontier is connected to the software side of neural reality, that has an impact on how we perceive the physical reality of science.
For example, consider two opposing political parties looking at the same social data. Each will draw different conclusions, using the same proof. This is due to an overlap of external with internal reality, that then impacts the philosophy of science. Also consider, man made climate change and how different scientists see this differently. Religion deals with this software side.
Genesis, in the bible, is less about physical reality, as it is about the software side of brain, impacting how we collectively perceive external reality. Science theory is always evolving, yet at each point in its evolution, humans think they are looking at the final version, due to the software side coming to a collective focus. God ruling the realm of mankind is sort of a metaphor for this affect.