What are atoms comprised of, and what physical properties do those component parts have, independently of each other? Because if only the arrangements of them exist, doesn't that throw into question, the concept of the physical as fundamental?
Well, electrons are, as far as we know, fundamental particles: they are not composed of anything else. They have a rather small mass, are electrically charged, have a spin of 1/2, etc. If you look at the particle Data Group, you can get a more complete list.
Mass, for example, relates both to how the particle responds to forces and how much gravity it produces. It also links the energy and momentum in any reference frame.
Protons and neutrons are made, primarily, of up and down quarks (with a small percentage each of strange quark), but most of their mass comes from interaction between those quarks through the strong force, which is mediated by gluons. The up and down quarks have different interactions via both the strong and the weak nuclear forces, are electrically charged by different amounts (and different than the electron). The gluons are also subject to the strong force in addition to carrying it. They are uncharged, so don't interact via the electromagnetic force, etc.
So, no, it is not only the arrangement, but HOW the different particles interact. Both aspects are crucial for the end results.