This is a great example of why it is important to recognize the difference between methodological and philosophical naturalism.
Methodological naturalism should acknowledge that there is a limit to what can and cannot be studied by the tools we have available and should acknowledge that it is unqualified to answer questions pertaining to the latter.
In both of these quotes, the respective authors are not making a distinction between “MN” and “PN” and are referring to the inability of “MN” to answer questions beyond its scope.
I believe when applied properly (and recognize that this is frequently not the case), MN is simply the best approach to answering physical questions and by no means any sort of attempt to keep the “bad guys” out.