I would assume so as well. You are making my point for me: that methodological naturalism would be intentionally blind to whatever supernatural processes may have preceded the operation of natural processes.
Nor do I. And for this reason, I do not understand those who say from the standpoint of science, “If the earth had been created in six days by supernatural processes instead of over 4.543B years by natural processes, we would see the evidence of it.”
Even if you correct me and say, “No, what we’re saying is that we do see evidence that the earth was created over 4.543B years by natural processes and therefore we know by this that the earth could not have been created supernaturally in six days.” My response to that would be “On what basis can you claim to know that the two are mutually exclusive?” Methodological naturalism - by design - cannot tell you. The most common answer I receive is a theological one: “Because otherwise God would be deceitful.” But I think this has been demonstrated to be a questionable conclusion (see Things are not as they seem).