What we perceive through our senses, is information about what is solid(hard), soft, liquid, gaseous, introspective, and positional. Therefore anything that stimulates our sense organs must exist outside of these sense organs. Our brain is a physical organ that is DIRECTLY connected to our sense organs. It can only detect the outside reality through these sense organs. All sensory inputs are compartmentalized by the brain, to represent its best guess interpretation of what the physical reality looks like. At no time does a physical reality exist within the brain, physically. At no time is a physical reality objectively observe. We are all physical biological organisms trapped within a subjective perspective of reality. Only without our senses, would our subjective reality become an illusion, or even exist at all. With our senses only the reality that is represented by our mind is an illusion, not the reality that the mind is representing. This can be easily tested. Just cover your ears, hold your breath, and close your eyes, and the brain's representation of reality will disappear. Since it is the representation, and not the reality that disappears, it must be the representation that is the illusion, and not reality.
At the Macro level of reality, we are not talking about one atom and the space between the electron(not photon) and the nucleus. We are talking about a trillion, trillion atoms being held together by the strong and weak fundamental forces of nature. As well as the EM forces. Hence we don't fall through the earth, or any other solid object. Also, light doesn't reflect off of empty space. Neither are our sense organs stimulated by empty space. But you are correct, at the Quantum level atoms are mostly empty space. Claiming that because all matter is composed of atoms, and all atoms are composed of empty space, therefore, all matter is really empty space, IS AN OBVIOUS FALLACY. Water is a liquid, water is composed of 2 gases, therefore water is really a gas. I think you can clearly see the logical flaw.
The early Universe was certainly very hot. So hot that not only could matter not form, but even light(photons) could not escape the heat. But this Universe was never sentient. It had no purpose, or higher design. We are simply the product of order out of chaos, if you will. Our evolution is the product of trial an error, chemical evolution, luck, and the laws of probability. Considering the fact that 99.999% of all creatures that have ever lived on this planet, are now extinct. We are the prodgenies of a generation of survivors. Or, do you think there were no other Hominids before modern man?