Actually I have been studying this topic for a while as well. I came across some good arguemnets that actually support the idea that metaphysical naturalism is a logical position to take under methological naturalism.
If one takes up the methodological position they must exclude anything non-physical or supernatural. It is not permitted as allowing this means allowing supernatural as a possible cause and explanation. But as the scientific method is based on evidentialism it is equating what someone believes with evidence and verification. Along with naturalism (only being about physical stuff) it is saying that only the physical will be included in those explanations and that the physical is what makes up reality.
So this position goes beyond the mere method as a tool and has attached an ontological claim and a epistemic position about how we have to explore, verify and understand reality. Thus this is also taking a metaphysical position as it supposes that reality/naturalistic causes are only physical and material.
So check out this paper and let me know what you think.
Methodological naturalism is based on the presupposition of causal isolation of the natural and the supernatural worlds. Methodological naturalism implies that only propositions supported by empirical evidence are reliable. The methodological naturalist is committed to the claim that the scientific beliefs which constitute their scientific knowledge have been justified by their perceptual beliefs and their entailments.
So the epistemological implications of methodological naturalism lead us to a version of “Evidentialism”, according to which the epistemic justification of a belief is determined by the quality of evidence that the believer has for that belief (Feldman and Conee 1985, 15).
From this point of view, being epistemically obligatory is equal to being epistemically justified (ibid., 19); and, conversely, just as relevant evidence obliges us to believe a proposition, the non-existence of any evidence compels us to deny that proposition.
Thus, evidentialism and naturalism excludes revelation and religious experience in justifying our beliefs, and admits only sense perception as the source of evidence; so it can be viewed as an expression of the epistemic basis of methodological naturalism.
“Naturalism rules out the possibility of recognizing any supernatural and non-physical cause has anything to do with the natural order of things. Hence, someone who accepts methodological naturalism has no option but to deny the existence of the sorts of supernatural entities. This worldview is exactly what at the outset we called “metaphysical naturalism”.
Methodological naturalism is the only reliable and also the most successful methodology for discovering the realities of the world; and scientific knowledge obtained using methodological naturalism expresses a naturalistic picture of the world, which among the different worldviews exclusively confirms metaphysical naturalism.
Should Methodological Naturalists Commit to Metaphysical Naturalism? - Journal for General Philosophy of Science