Okay, I think I get what the distinction is now (but if I understand you correctly, evolution was a weird example to choose, because of the vastness of the evidence in favour of that particular model).
So the distinction between metaphysical naturalism and methodological naturalism seems to be that the former says “Anything that exists can be measured objectively, even if we don’t know quite how,” where the latter says, “There are, or at least may be, forces in the universe that cannot be objectively measured.” Methodological naturalism supposes that such forces may account for such things as souls, ghosts, and other paranormal phenomena, whereas metaphysical naturalism dismisses such phenomena as nonsense and says that they can be explained scientifically.
Am I getting this right?
On the one hand, making an observation on the about something as fundamental as “Nothing exists that cannot be measured” seems like incredible hubris when we can’t even figure out exactly what dark matter is, aside from the fact that it has mass and it doesn’t interact much with light.
On the other hand, postulating that particular phenomena are the result of something that cannot be measured instead of something that has not yet been measured seems like defeatism: “Don’t try to study what consciousness is; such things are beyond the reach of science.”
I really don’t like either.
Stick me in whatever the “I don’t deny that there may be things out there that we can’t understand or measure, but that’s no reason not to try to quantify them” camp calls itself.
