The the motive for a "methodological naturalism" is in some instances warranted. There is an analogous method taught in literature classes, which the famous poet John Keats called "negative capability." It has something to do with suspending judgment for the sake of being open to observation. I guess the problem is that scholars get stuck in their method being so happy with their success. This is not particular to scientists. This is a habit of the mind, a particularly nasty one.
I readily grant your point, and agree that "it has something to do with suspending judgment for the sake of being open to observation." IOW, to suppress "subjective" elements, so to enable a purely "objective" assessment of the data.
I have a funny story that sheds light on this issue. Albert Einstein and Neils Bohr were very close friends. Einstein as you probably know never accepted quantum theory, even though we was one of the earliest contributors to its development (i.e., his work on light). He used to tease his friend Bohr, who insisted that it is the business of science to make descriptions of observations, and you can't describe what you haven't actually observed.
On that basis, Einstein would say, "If Niels does not observe the moon in the sky, then for him the moon does not exist." Therefore, Einstein argued, Bohr was relentlessly subjective in his approach to science.
But this is to misunderstand Bohr, I believe. Bohr was amazingly epistemologically zealous -- presumably in the attempt to keep things as objective as possible. He emphasized direct observation as the sine qua non of scientific investigation. He knows the moon is up there in the sky. His point was he couldn't say anything about it as a scientist until he had observed it for himself. Only on that basis could a scientific description be made.
Bohr (and Einstein) offered some of the earliest descriptions of the so-called observer problem. It is evidently manifest in both relativity and quantum theory. However it seems clear to me that the observer problem is "alive and well" in science dealing with the Newtonian "macroworld" (our four-dimensional spacetime world) as well, by simple analogy.
If Bohr is right -- epistemologically speaking -- then it needs to be recognized (IMHO) that even such a widely-accepted theory as Darwinist evolution is to some degree compromised as science, because it rests so much on things that no one has ever directly observed. The accretion of subjective elements is bound to occur over time if that is the case. Thus philosophy inevitably gets smuggled in through the back door, in the end....