Neuroscience actually answers a lot of the questions you've posed (though, admittedly, not all.) Everything from being hugged as a child to traumatic brain injuries influences the development of the brain, encouraging activity in some lobes while discouraging activity in others. Neurological scans confirm this; even in identical twins, there are differences in how their brains function. People often cite nature versus nurture in a way that implies each is mutually exclusive when, in fact, each has a factor in determining who a person is and/or will become.
This is why I believe that choosing to let "Johnny" take over is more of a merging of "V" and "Johnny" than "V"'s actual death. Yes, the biochip overwrites "V"'s psyche, but in the end "Johnny" still doesn't act like the original Johnny Silverhand. I believe this is due to the fact that the original V's brain has already developed in a certain way. It processes information in a way that's different from OG Johnny, just like my brain processes information in a different way from, say, a serial killer. A serial killer could encounter someone who fits their preferred victim's MO and be inspired to hurt that person, whereas I could encounter that very same person and think that they were rather charming. Two brains, two different responses, all facilitated by the way each processes and reacts to stimuli.
OG Johnny's memories are there, but those memories weren't actually experienced, and thus couldn't have impacted the development of OG V's brain. Muscle memory, established neural pathways, information processing and retention, all of those are still being handled by a brain that was influenced by OG V's experiences, and thus each new experience will elicit a different response than if "Johnny" were still in OG Johnny's body. The player is neither OG V or OG Johnny when "Johnny" takes over. They're Johnny Silverhand's memories and personality, filtered through a brain cultivated by the choices and experiences of OG V.
I don't like any of the endings (or rather the feeling they give me), but if I had to choose the least "bad", I would choose this one ... RELUCTANTLY! I thought about this, when I first saw it, and I have to somewhat agree. This is
kind of a "merging ending", because V obviously influenced Johnny in such a way, that he effectively becomes a different person. So much so, that he even can finally let go of his hell-bent hatred for Arasaka and the city itself. Additionally he has to live with the constant reminder of V because, as he says, he has to live with his/her "fcking face". Not only that, as you point out, but also with certain other biological features, the brain being just one of them (think about playing V as female!). He also had literally palpable access to V's memories, and memories are an essential part of a person's individuality.
In the end however, this is the weakest variant of a "merging" a writer can come up with, because despite all these points Johnny still identifies as Johnny, and not as someone else, someone new. We, as an external spectator can ask, "
Johnny, could it be that you've become someone else entirely?", but he does not raise this question. He very much keeps mentally seperating himself from V, as can be seen by him puting V to rest, by "burrying" her pendant, and saying things like "
I have to stop talking to you." and "
I cannot wear this any longer.". He clearly misses V. At least two times he invokes his/her name with a heavy sigh. So, what I wanted to say with this - for me this is not a satisfying "merging", because Johnny doesn't embrace it, and the part of V's conscience is missing entirely.
Hmm ... Having said that, however,
maybe the Arasaka ending can also be seen as a
kind of "merging", albeit one that is a little bit stronger. After all, there, we hear Johnny creeping into V's dreams, trying to again influence her, implying something of his conscience could still be within V ...