If you don't like that terminology, what do you prefer? If methodological naturalism is not an acceptable basis for scientific inquiry because it is "derived from philosophical naturalism", what philosophy do you propose to derive a methodology from, and what would that methodology be?
I didn't say methodological naturalism was "unacceptable" because it's "derived from philosophical naturalism." It is what it is. These are just doctrines. As such, they assume a great deal without validating their assumptions. They simply aver something — there are only natural causes in nature. No other causes can exist by definition. Thus the doctrine "reduces" the world to our expectation that it is the product of natural causes only.
If this were actually true, then all would be just hunky-dorey. Unfortunately, no one really knows whether it's true. At the end of the day, it is simply a faith statement. For the non-existence of causes other than natural ones has never been shown; I doubt it can be shown. Methodological naturalism just takes it for granted that the statement is true.
Thus an epistemological problem arises.... How sound can our knowledge of the world be, really, when we are already "editing" the world down to the size of our expectations, in advance?