Physical alterations/robot parts

This book has been somewhat hard to keep up with because I don't understand most of the ways these people think. I don't recall reading anywhere specific where R outright says whether or not they have robotic components to them. There are a couple of entries that have interesting descriptions on a couple of specific characters.

First, on page 43, when R is telling D that he had to versify a court sentence. R says, "I looked at his tightly locked little valise, thinking. What is he turning over there, in that little box of his?" Second example is on page 61, once again during a conversation between R and D: "He frowned and rubbed the back of his head--that little box of his with its strange baggage that I did not understand." Is he being literal in these descriptions? Or is he simply referring to R's mind as a box? I couldn't really answer these questions for myself.

Another description like this one in the book that makes me lean towards the conclusion that he's being literal is on page 46 during the court sentence. R is describing the Benefactor, "So with these heavy hands, still calmly reposing on the knees. And it was clear-they were stone, and the knees were barely able to support their weight." This makes me think that these people definitely have body parts that aren't their own.

The last example I've come across so far is when R is in the underground tunnels under the Ancient House on page 86, "Or suddenly I feel that I must glance back, but it's impossible, no matter how I try, my neck is rigid, locked." Is it locked and rigid because he's so afraid of being in the dark tunnels and doesn't know what's going on? Or is he physically incapable of turning his head because his neck is really locked?

It makes me think that if some of these people have physical abnormalities that have been imposed upon them by the One State, how long before it is a requirement for everyone? Or, even more drastically, how long before they replace all humans with robots who can actually be programmed to do as the One State pleases?

Overall, I was confused about whether or not these descriptions are being literal and these people have been physically altered by the State, or if they were simply descriptions (which I doubt because R is so technical and straight to the point--for the most part).