Quantum chromodynamics is actually pretty similar to Maxwell's equations of electromagnetism. The big difference is that unlike photos, gluons interact with each other. This means goodbye to linear equations and simple planewave solutions. One can't even solve the equations in empty space, and only recently have supercomputers become powerful enough to make good, quantitative predictions about things like the proton mass.
How could something so remarkably stable and functionally indistinguishable among its peers also be so complex?
To your question, I think there is an elegant answer actually; most composite particles in QCD are unstable. They're either made out of equal parts matter and antimatter (like pions) or they're heavier than the proton, in which case they can decay into one (or more) protons (or antiprotons). If any of the internal complexities of the proton made it distinguishable from other protons, they wouldn't both be protons, and one could decay into the other. Quantum mechanics also helps to keep things simple by forcing the various properties of bound states to be quantized; there isn't a version of a proton where e.g. one of the quarks has a little more energy, similar to how the energies atomic orbitals are quantized.
One of the implications is that there are many interactions where most possible Feynman diagrams contribute non-negligibly. The advances in theory arguably have much more to do with improvements in techniques and the applied math used, such as in lattice QCD and Dean Lee's group for instance.
The study of these things, on the other hand, is genuinely complex and difficult. But that's epistemology, not ontology.