The whole Concept of him, not dying after he was killed was because he had a "profound attachment to the rest of his species" well actually to trinity, Trinity really had nothing to do with him living, it was him, it just looked better with trinity. but she had no real impact on him not dying. When the architecht says that "your 5 predossessors, were by design based on a similar predication.........which was ment to produce a profound attachement to the rest of your species, facilitationg the function of the one, while the others experianced this in a very general way, your experiance was far more specific, visa vie, love" presumably the others became the one because of an attachemnt to the whole of the humans, Neo became the one because of a similar attachment, visa vie Trinity, thats why he did not die.
Here's one that's out there.
No one dies in the matrix. After watching the matrix something has always bothered me. When people die in the matrix why doesn't their bodies or RSIs disappear.
The RSIs are mental projections of their digital self, if the mind is dead there should no longer be a mental projection, even if it is of a dead body. Therefore the mind is not dead it only believes that it is.
Neo's words to Trinity after she died "I know that you can still hear me."
In short the mind never dies, it only belives that it does.
Here's an idea...the matrix is programmed to keep them...if you are walking along with your best friend, lets say, and all of a sudden thugs from the hood take you two by surprise and shoot your friend. Would you be more or less calm if your friends body just disappeared after he died? while you are hysterical that your friend died, it would change everything if your friends body disappeared from right before your eyes. Thus, the matrix is programmed so that the RSI don't disappear. So people can have funerals. perform autopsies. grieve healthily. yeah, it does die. but it is left for aesthetic purposes.
just thought of another example. Michael Popper. He self-substantiated. he freed his mind without Neo or Morpheus. Thus, his mind was put back into his body. However, his family had a funeral. there had to be a body, as they knew where he died. If his mind is in his body, as it has to be for him to be alive, then what was left was not his mind, but rather, a shell, a body for his mind. it is not his mind though.
Your first paragraph was an idea I also had but then again I thought that if I were born into the matrix then if a body was to disappear on death then if the matrix was all I had ever known then I would accept that as normal.
Your second paragraph however I had not thought about at all, very good thinking. For this I would say that follow the sequence of events. Popper was dead and buried in the matrix before we see him in on the ship of the Neb. I know that it may seem arrogant but I stil think that I'm right.
Numo>> In short the mind never dies, it only belives that it does.
if the mind indeed thinks its dead, it will stop sending signals to your heart, lungs and other vital organs. when that happens everything stops functioning. your blood has stopped circulating, your lungs stopped breathing and oxygen is gone. the mind doesn't think its dead, it is already dead.