Limited methodology and ignorance of unknown variables are not assumptions of capital-s Science (i.e., methodological naturalism), but assumptions of a specific experiment(er). Which is to say that they are scientific hypotheses conditionally adopted above and beyond the basic assumptions of naturalism in order to enable specific theories and experiments. You can take them away without affecting naturalism, and so they have nothing to do with the lofty fundamentals you were discussing a few posts back. Like "evidence," the concepts of "methodological limits" or "variables" are not well defined absent the assumptions of methodological naturalism. The assumptions you are talking about don't stem from naturalism ("the nature of science") but rather from incuriousness. You can very well accept all of the assumptions of naturalism without assuming that any theory (or even all of science) is complete. To put it another way, Fleming didn't discover penicillin because he questioned the assumptions of naturalism. Rather, he questioned the assumption that mold wouldn't inhibit bacterial growth. At no point in that process was naturalism a limitation; on the contrary, it was the key at every step of the process, particularly the breakthrough step. Questioning the assumptions of a particular theory is a vastly different matter than questioning the assumptions of naturalism, and accepting naturalism in no way encourages a person to uncritically accept all assumptions in science.