Then, humans started coming with very silly ideas about the model actually being the reality it models.
Humans aren't real. They are merely a hodge-podge of organs acting in concert which obey the standard medical model. Organs are simply groups of cells that act in concert, which obey the standard biological model. Cells are made of molecules which obey the standard organic chemical model. Molecules are merely structured atoms obeying the standard chemical model. Atoms are composed of bosons, fermions and hadrons, and hadrons are small clumps of quarks I think, and all these subatomics obey the standard nuclear model (aka the "Standard Model"). Bear in mind, all matter by volume is 99.999%+ empty space, and that none of the models I mentioned are empirically real; they are abstract. We just use them to help explain our observations, and they help the math come out neat. Thus, as humans are comprised of aggregates that are also comprised of more fundamental aggregates, etc., they're mostly just a convenience of language.