Science does not assume naturalism in it's epistemology, it assumes it in it's methodology. It is open to the supernatural and does not say that there is no God and no angels etc.
As we know, science has not the tools to find the supernatural and any discovery of mechanisms to explain the natural world does not eliminate God or the supernatural from. It is just that the God of the gaps idea was wrong to begin with and God was not sitting in heaven and throwing lightning bolts etc.
God is the answer to the who question and science finds a "how" answer. And imo science goes too far in with the how answers and steps over into the sphere of theology,,,,,,,,, not on purpose however, it is just that it is wanting to find a naturalistic explanation for things that God has done and ends up defining things in a naturalistic way. eg science can see what chemicals do and what a brain does and ends up defining life and consciousness in terms of chemicals. All science can do is describe how a body might have evolved chemically and what a brain does when it works. It cannot say what life or consciousness it.
In this way science starts trying to fill gaps with naturalistic answers when there really aren't naturalistic answers.