After you have gone to all the trouble of writing all that, Danny, I am going to be very cruel. I do not think that Tezuka or anyone associated with Atom worries about these things.
This reminds me of a literature class I took a few years ago. We would sit around (well, actually it was a online class) & discuss characters' motivations, & even try to determine what messages the author was trying to convey through the story.

All this was assuming he was writing for such a purpose, rather than some other reason.
Getting back to your post, old systems are upgraded with new components. The B-52, was one such system. These aircraft were in service for what, 20, 30 years? Eventually the cost Vs. benefit fraction of upgrading becomes unacceptable. So, they design the B-1 then the B-2. In Atom's case, his psychological and other such intangibles are what makes him 'him.' These are the irreplacable parts. Remmember what Bender became when he fell into the fountain of youth? He was reduced to a compact disc.

This was his essence, it was what he was that made him recognizible as 'Bender,' rather than the other robot who was physically identical to him except for having a beard.
I remember a FF comic in which Dr. Doom was fryed by the Silver Surfer. He would have been dead were it not for his swapping consciousness with some other guy. Now, Dr. Doom was in this other guy's body, & he was having a hassle going into his own home, because his security devices did not recognize the other guy's body.

He was Dr. Doom, regardless of what body he was 'in.' Likewise with Atom, when they bad guys suckered him into an 18 year-old version of 'himself,' so they could steal his original body, & use it for crime, he was forced to destroy it (Astroboy Stolen). Yet, even in a teenage body, he was still 'himself.'
Tezuka explored this topic with his
Marvelous Melmo series. In this, a (10 1/2 to 11-year old) girl could change her body's appearance by eating 'candy.' She could age it by 10 years with each piece of blue (or was it red?), and cause it to anti-age with the other colored candy by 10 years. regardless of whether she appeared to be a 19 year-old, or a granny, she was Melmo, and possessed Melmo's 11 year-old personality, understanding, maturity, etc.

In fact, by eating a combination of these candies, she could even transform into various animals. But whether she was a cute little puppy (complete with pink ribbons tied into bows), or an elephant, she was still Melmo, an 11 year-old girl (or was she 10 1/2?

).
Melmo episode guideNote that Melmo matured (naturally) into a beautiful woman in the end, just as she used the very last of her candy.
Atom seems to understand the concept of death, but would he have trouble accepting the death of friends? Again, I think this is asking a question that his creators (Tezuka et al) did not worry about. Granted there was a manga story in which he realized that he would always be a kid, even when his human friends were grown, but I do not remember him thinking about them dying of old age. B)
Compare this to the Tachicomas' (Ghost in the Shell: Standalone Complex) discussion about it. They realized that they could not die, because they were not alive in any biological sense. They also admitted that they really did not understand the concept itself. As their AI began to develop into full-fledged person-hood, they did worry about their masters' denying them their person-hood, apparntly because they feared the Tachicomas would not obey their orders, or would go off on their own, seeking goals other than theirs.
