Yes as far as I understand it they did.
According to the paper methodological naturalism takes what they call the “Stringently Pure Closure” (only physical causes are allowed) ones and nonphysical/supernatural entities are not allowed. The only propositions regarded as reliable are those supported by empirical evidence.
So therefore the methodological naturalist is committed to the position that the scientific beliefs which constitute their scientific knowledge have been justified by their perceptual beliefs about reality. As the paper states the epistemological implications of methodological naturalism is that it dictates beliefs about reality and the natural world.
So methodological naturalism is not just about being open to search for any possible causes of natural phenomena and reality but only particular causes and justifications about how we should see and know reality and nature and therefore as the papers conclusion says
Our purpose in this paper was to prove that commitment to methodological naturalism necessitates the adoption of metaphysical naturalism.
I used this particular paper as you mentioned that methodological naturalism did not lead to metaphysical naturalism so I was just pointing out how the paper made a good reasoned and logical case that it does.
The main arguments for rejecting methodological naturalism leading to metaphysical naturalism are that science cannot investigate the supernatural because it is a different type of cause and should be kept separate. Another is science includes the supernatural and finds it’s something that is impossible to determine or there’s no way to distinguish the physical/natural from the non-physical/non-natural and thus ruled out.
There is some debate over what methodological naturalism represents for which some claim it is being misrepresented and is only about method. Another argument is that science is seen as something that has proven itself over time and therefore is a justified basis for determining things.
Methodological naturalism and its misconceptions
https://www.researchgate.net/publication/313267955_Methodological_naturalism_and_its_misconceptions
“Grist to the Mill of Anti-Evolutionism: The Failed Strategy of Ruling the Supernatural Out of Science by Philosophical Fiat.”
Grist to the Mill of Anti-evolutionism: The Failed Strategy of Ruling the Supernatural Out of Science by Philosophical Fiat - Science & Education
Methodological naturalism in the sciences
Methodological naturalism in the sciences - International Journal for Philosophy of Religion
These positions have problems though. As the paper I linked said science claims realism so any open investigation of finding reality/nature has to include all possibilities and not what it thinks is real. Supernaturalism and the nonphysical have often been misrepresented when there is a lot more to it and there are ways to determine things indirectly.
Science is in control of the determining the mothodological criteria for which they contradict by allowing non-verifiable and nonphysical ideas themselves. They are restricting things to evidence, how to investigate and what is classed as evidence and what is classed as physical and non-physical. By doing this methodlogical naturalism is more than a method and is also a metaphysical position.
As another paper I linked earlier in this thread explains all this. It gives examples of how science already includes nonphysical and unobservable causes and influences yet rules out certain types arbitrarily. How the verification method is not what people think and that if applied would rule out many theories already accepted by science but can also include many nonphysical ideas science chooses to reject. The supernatural and nonphysical doesn’t have a chance as it is not allowed a priori. That’s the metaphysical position taken by methodological naturalism.
Replacing Methodological Naturalism
Replacing Methodological Naturalism - Metanexus