I'm not the author of the comment you'replying to but I'm pretty sure that consciousness is more than atoms. Feeling pain can't be explained as an interaction of physical particles. You could describe the chemical processes in the brain accompanying pain to very high detail. But at no point you can't explain why does it hurt so much when the atoms in the brain are in a specific state.
Because physics doesn't even have the language to describe the feeling of pain. Similarly, physics doesn't have a language to describe how "green" looks, it can only describe the frequency of green etc.
Both, it doesn't really matter, basically any state of consciousness. Physical processes in brain accompanying physical pain may be understood very well. But we don't understand the mechanism that translates the physical state of brain matter to the hurting feeling. Why does it hurt, when we arrange brain's atoms in a specific way?
Your explanation doesn't make sense. We know that there are people who
a) don't exhibit emotional pain or very little compared to "normal" (sociopaths/psychopaths)
b) are autistic and have "...difficulty with “subtle emotions like shame, pride, things that are much more socially oriented” 
c) people with Congenital insensitivity to (physical) pain, some of whom experience the condition due to excess production of endorphins in the brain
You seem to suggest that the question "but why does it hurt" is somehow mystical or metaphysical. I don't think it is. It hurts because your brain is wired so that it does. If it is wired otherwise (as in some people it is) then it doesn't hurt.
Yes but the question is, why does it hurt when the brain is wired in a specific way. What makes some positions of brain's atoms painful? Physics doesn't even have a way to scientifically define what "feeling pain" is. Physics can only define physical processes accompanying feeling pain.
"why does it hurt when the brain is wired in a specific way?"
Because organisms that evolved to avoid that thing we call pain survived long enough to pass on their genes, whereas those that didn't got burned up, crushed or in other ways extinguished?
In other words an aversion to that thing called pain gave an evolutionary leg up. And it seems that this aversion is fundamental to life since every creature has a tendency toward self preservation.
There are many examples of people who enjoy physical pain and perform cutting even down to bone, and sometimes including amputation. Clearly this is an example of brain wiring which is not beneficial to the individual and, in extreme cases will self-filter out of the gene pool.
We can describe the entirety of an operating system down to its individual ones and zeroes. Do you posit that some irreducible "Tuxness" state exists that computer scientists just refuse to acknowledge?