Yes it can. In fact it cannot be otherwise. The content of science is what it is. It is an objective reality that a certain idea, theory, principle or presupposition is or is not employed or implicated in scientific research as it is actually conducted. Now we might argue in certain gray or unclear instances about what ideas have actually been employed, but we'd be arguing about the REALITY of the situation, not pointlessly parading incommensurable "philosophical underpinnings attendant to each observer".
Do you even realize that you sound EXACTLY like a leftist/deconstructionist who denies that ideas have objective implications.
Objectivity is a fine thing. Unfortunately it is subject to human interpretation. If you think science is all the better simply by declaring itself to be "objective," or by declaring that "all observable phenomena may be classified as natural," then you are seriously unaware of its limitations while operating with a mode of science that is beyond its cherished "falsifiability."
There is no such thing as a human observer who is not guided by some set of philosophical assumptions. Anyone who claims himself to be completely and totally objective is a liar, because objectivity by definition resides outside of the observer. The observer cannot go outside himself, but is constrained by all that comprises his personal inductive and deductive skills.