You and I agree on this point....now we have stepped over into epiphenomenalism.....not naturalism.
epi... who?
I think I once knew a girl named Epi, and yes, she was phenomenal, but sadly, I couldn't hold her... ;-)
My term is methodological naturalism, and it describes classical natural-science, which hoped to find natural explanations for natural processes.
In methodological naturalism science is simply a tool box we use to disassemble, study & reassemble the natural world.
It's intended to be useful to people of any religion, or no acknowledged religion.
In your term, atheistic "metaphysical naturalism" aka "ontological naturalism" and "philosophical naturalism" we take up our tool box and place it on an alter so we can bow down to worship it.
So a simple tool box has become our god and religion in metaphysical naturalism.
That's why people with any religious feelings whatever find it... well, uncomfortable.
So of course I agree with classical methodological naturalism but not our new-fangled atheistic metaphysical naturalism.