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I've heard your argument on this before, and probably responded similarly before, but the special status you attribute to matter in this respect is arbitrary. ALL scientific concepts (certainly all significant ones) are theory laden in the same or similar respects.

Of a truth all sciences deal with theories - but physics all the more so, because theory is what physics is "about:"

Many biologists consider physical laws, artificial life, robotics, and even theoretical biology as largely irrelevant for their research. In the 1970s, a prominent molecular geneticist asked me, ‘Why do we need theory when we have all the facts?’ At the time I dismissed the question as silly, as most physicists would. However, it is not as silly as the converse question, Why do we need facts when we have all the theories? These are actually interesting philosophical questions that show why trying to relate biology to physics is seldom of interest to biologists, even though it is of great interest to physicists. Questioning the importance of theory sounds eccentric to physicists for whom general theories [are] what physics is all about. Consequently, physicists … are concerned when they learn facts of life that their theories do not appear capable of addressing. On the other hand, biologists, when they have the facts, need not worry about physical theories that neither address nor alter their facts. Ernst Mayr (1997) believes this difference is severe enough to separate physical and biological models: "Yes, biology is, like physics and chemistry, a science. But biology is not a science like physics and chemistry; it is rather an autonomous science on a par with the equally autonomous physical sciences."
H.H. Pattee The Physics of Symbols: Bridging the Epistemic Cut Biosystems. Vol. 60, 2001, p. 5–21