Reality doesn’t have layers that we know of…

…is an unfalsifiable claim, which means it has no place in this discussion.

And the whole point of physics and science as a whole is to assume reality is constant

Because they play a special role in existential “reality”. They illustrate that reality can have layers. The fact that there’s a hierarchy among the layers does not disprove the notion of higher layers. If anything, the pattern would seem to indicate that there’s more layers.

May I not reply with a parable? The human mind, no matter how highly trained, cannot grasp the universe. We are in the position of a little child, entering a huge library whose walls are covered to the ceiling with books in many different tongues. The child knows that someone must have written those books. It does not know who or how. It does not understand the languages in which they are written. The child notes a definite plan in the arrangement of the books, a mysterious order, which it does not comprehend, but only dimly suspects. That, it seems to me, is the attitude of the human mind, even the greatest and most cultured, toward God. We see a universe marvelously arranged, obeying certain laws, but we understand the laws only dimly. Our limited minds cannot grasp the mysterious force that sways the constellations.

1: By the very definition and premise of the laws of Physics, everything that can interact with anything else can only do so via the laws of physics. This is just as fundamental and innate as 1 + 1 = 2.
2: A full philosophical zombie is completely physically identical to a human.
3: Thus, a full philosophical zombie cannot exist, because only physical things can interact or affect other physical things.

As for the speed of light and ether possibilities, I’m pretty sure that’s a no, as it’s not compatible with the standard model, quantum mechanics, and general relativity.

Then by a similar argument, engineering, philosophy, video game design, biology, art – are all physics.

No, but it can be reduced down to nothing more than mechanical actions. Any series of mechanical actions, no matter how complex, should only result in a philosophical zombie. A philosophical zombie is the logical, and only conclusion you can arrive at in a purely materialistic universe.

. Simply put, I want you to prove it. You complain of unprovability, but I don’t need to prove to you that my qualia exists – I directly experience. I see a laptop screen and feel keys under my fingers – I know I experience qualia, what I want proof for is that you can physically show why that being does more than act like it feels. Simply put, you cannot. You can only show an increasingly complex system of how something behaves, but you can never show it actually feels.

Our brain isn’t a set of mutually independent intelligences, but it is, nonetheless, a physical system, and there’s no reason why any conceivable physical system should give rise to something that feels, rather than something that acts like it feels.

I imagine you think that if there’s no physical difference, then there’s no difference, thus there are only physical things – but this is a circular argument, and I reject the connection in-between “if there’s no physical difference, there’s no difference” in this particular case, because there is a difference. Namely, as has been explicitly stated, one feels, and one does not. You may make an appeal to a materialistic philosophy to refute this, but that appeal will not work, as I believe this particular case is an actual breaking point that disproves materialistic philosophy.

Any world view is nothing but a structure that strives to model reality as accurately as possible – to make sense of it – but exists, being built up around certain key axioms. Foremost of those key axioms, to me, is my own existence. I think it impossible for me not to exist, as I directly perceive my own existence. I feel, therefore, there is something that feels. To me, that is the first axiom of reality.

The second axiom is the physical universe I observe, because I know this one can be false. I can observe a universe that “isn’t there”, or more precisely, that is inconsistent with my other experiences of the physical universe. I quite love that, for some inexplicable reason, it follows predictable, logical, PERFECTLY consistent laws, and that I keep coming back to this one each time I wake up – or so my memory tells me. The elegance and beauty of its consistency and logic are the matter of a physicists’ study.

Nonetheless, I don’t believe, because I don’t know, if it is the only possible universe. Could we exist in a universe with a different cosmological constant? How about one where there is no speed of light, and light particles and such move along in an ether? How about one of the universes constructed in the circuits of our creation – one of finite entities and pure logic (it is a little disturbing how much our own universe could possibly fit such a description).

That is yet another reason I hold physical reality as secondary. It is not fundamental, and I see no reason to assume that it is apart from its own existence. So I’m willing to accept that things may lie beyond it, because to me, reality extends beyond this universe. Things like mathematics and my own existence transcend it. Every night I experience a universe separate from this one – a universe where I could equally be presented with an equally logical “universe” – one where the waking world is death, for example, and nothing is known except that those who “wake” vanish from the world forever, and leave their avatars behind.

The mind-body problem is a Physics problem, as Physics contains all interactions under [its] purveyance.

our brain is not a set of mutually independent intelligences…

any being advanced enough to be 100% indistinguishable from a human via observing behaviors would automatically have qualia themselves

1. “I think, therefore I am”. More precisely, “I feel, therefore there is something that feels”. This is qualia.  
2. We observe a physical world around us.
    
   However, #2 is as fallible as our senses. #2 leads us to believe whatever we dream of, no matter how insane the dream is. #2 is not a valid way to disprove #1. Therefore, the failure to identify #1 within #2 does not mean that #1 doesn’t exist, it just means that #2 is incomplete. Ergo, there is more to the universe than is physically observable.
    
   Another illustration of this is qualia’s existence. The Chinese Room thought experiment more or less proves that you can have something that interacts with the world as complex as a human mind, yet there is absolutely no physical reason why it should “experience” as we do. A careful enough study of the brain reveals it is much the same way. Simply put, we should mechanically carry out whatever actions we do without actually feeling anything.
    
   Yet here I am, experiencing, despite its physical impossibility.
    
   Simply put, there is no physical reason we should be aware as we are, yet we are. We should all be philosophical zombies - beings that interact in a complex way and act as though they feel, but do not. But we feel, and this is a direct observation.
    

because it’s hard coded into the theory that nothing but the physical laws therein influence said probabilities.

I take free will to be on the same level of qualia – something you experience and thus know exists, but isn’t physically provable (for that matter, every unique experience of qualia is that way – the feeling of pain, love, joy, confusion, surprise, excitement, etc. etc. etc.).