Evidently they are differentiated to show that one — methodological naturalism — has become the term of art for the currently reigning "scientific method." The emphasis is on "method," or manner of proceeding in the investigation of nature. The latter — philosophical naturalism — is the doctrine that justifies the method — that doctrine being that all natural objects can have only natural causes. In any case, the former is derivative from the latter.
Does there exist a methodology derived from philosophical supernaturalism that can be used as a framework for consistent scientific investigation?