On Quantum's Universality

Often when I am thinking about the foundations of quantum theory, I am struck by the universality of the theory. Quantum theory (or its related cousin, quantum field theory) applies generically to all physical systems (disregarding the transition to some “classical” theory and of course, difficulties with both QCD and gravity.) Thus we apply quantum theory to our basic theories of physics, electromagnetism, the weak force, the strong force, but we also apply quantum theory to simple atoms and complex molecules, to single electrons and electron gases in metals, etc. Quantum theory is the universal language we use to describe any physical process. If we are thinking about ways to explain quantum theory, then this universality is a bit mysterious: the explanation had better apply to all of these different physical systems and that seems like a lot of work! Of course, this reasoning is flawed: it seems the universality is an illusion. The reason we can describe a complex molecule by quantum theory is that the fundamental constituants of that molecule obey quantum theory. Separation of different energy scales (and other scales, like localibility) allow us to ignore some of the constituants details, and the complex system behaves like a quantum system. So really any explanation of quantum theory need only apply to some basic level of physics (where this level is I refuse to speculate.) While quantum theory appears mysteriously universal, this is an illusion for those persuing understanding the mystery of the quantum.