As note to the Alt can record engrams - that's an actual point in regards to the copy existing while the original keeps existing. Meaning it difers from transfering and is actually copying. - It's on the same not as your Saburo note.
Which is why i get the feeling that CP2077 is somewhat of a retcon.
Though if you read up Soulkiller in the Cyberpunk wiki - even that wiki is speaking out against the immortality and "transfer instead of copy" idea of the CP2020 sourebook somewhat. -edit- So either a bad editor; or also some retcon in CP Red, given that gets mostly quoted?-/edit-
What's interesting to note, imo, is how unclear the actual Relic chip gets when you take the transfer idea from CP2020.
-> Why use a Relic 1.0, which isn't overwriting things, but allowing communication with someone, when you don't need such a thing, as you easily already should be able to communicate with an engram?
-> Why even have a Relic 2.0, when you can easily write engrams into the brain directly? ; Logically that wouldn't be able and the actual DNA problem (or some such) of. But then again, as some Soulkiller descriptions (going from the CP wiki) describe the copy process as frying the actual brain of it's victims - therefore likely destroying the original patterns - how was it supposed to work beforehand?
So. Again it looks to me, as if it worked differently originally and CP2077 writing changed it or something.
The thing with Relic is that the public version of it is solely the version 1.0, and its own use as a "tool of immortality" and "comunicating with the construct" is a massive PR stunt to lure those wealthy and powerful across the board to be willingly subjected to Soulkiller AI, having their mind essentially extracted to Mikoshi and to Arasaka servers. The thing is, if I remember correctly, Arasaka normally uses Soulkiller to extract data and minds of people, including competitors and those whose talent is too valuable to suffer death, for the corp's own use. AFAIK they get the person (either through Net, or physically into the same rig they put Johnny into), then hit them with Soulkiller, and then they dispose of the body. When they go for the Relic and "Secure your Soul" program, the real reason behind it (at least acording to Mike Pondsmith's ingame alter-ego, Mike from Morro Rock) is to learn all secrets and leverage they can from people they normally wouldn't be able to touch. Basically, they would store engram through Mikoshi, then copy it on the relic chip so their client get their loved one to converse with, and then they interrogate the copy (or more precisely, they get into its memory). Relic 1.0 can't rewrite consciousness.
The version 2.0 of Relic, the biochip, though... that was Saburo Arasaka's pet project. It wasn't intended to be given to masses, Hellman himself says it. From what the game tells you, it was developed to allow one man, "the Emperor" himself, Saburo Arasaka, to become immortal by transfering his engram into a new body by rewriting its brain, and what you get ingame into V's head is a testing version with the most disposable engram that Arasaka has on it, that being one Johnny Silverhand, and V is actually the first one on whom it succeeds to even start to rewrite the brain without killing the body outright. That biochip is, in a way, unique, or at least it is of a very, very limited production.
Now the murky, theory part:
As for the DNA problem, I bet it wasn't supposed to be used on a body with much different DNA... the game doesn't specify it, but I guess those original failed attempts were using a cloned body (even if in the "Devil" ending, the one in which you side with Arasaka, it is discovered that a direct relative can be used for this... which leads me to a theory that Arasaka had to clone Johnny's body for those tests). The biochip uses nanites to rewrite host's brain while being pretty agressive about that, and the DNA compatibility is there probably to assure that immune system of the body won't reject those changes.
And now full-on theory time:
Dunno about the copy vs. tranfer aspect, but from what I was able to gather, Soulkiller, in its current form, leaves body of its victim seemingly braindead, with blank mind, as in the process of forcibly extracting all the data from one's brain essentially destroys what is written in it. The version of 2077 (or 2023, for that matter) might not be the same as what Alt was forced to write for Arasaka back in 2013, as Arasaka had time to tinker with it, but it might not be that of a big deal.
Alt made a backdoor in the system, allowing her to return to her body if necessary (in a way reversing the process that Soulkiller uses to extract the data). The only weak point of that was that back then, the body had to be connected directly to the mainframe (Mikoshi wasn't a thing back then), and for the backdoor to work, this connection had to remain. But when Johnny made his rescue attempt and Arasaka used the program on her as she predicted they would, Alt's disembodied engram (copy, consciousness, whatever, the result was, in a way, the same...) got held up in her own escape attempt, so she was unable to start the process when her body got disconnected.
So, what happens to V during the three endings in which you storm Mikoshi (or four if we count the secret one and the one with Rogue as separate) is that the new, AI Alt gets access to the Mikoshi and then V connects to Mikoshi mainframe, and Alt hits him with the program, and then untangles the two personalities, creating a distinct engram of V (a copy of his consciousness, or personality construct, or whatever), and then makes the path through the backdoor in Soulkiller, writing back V (or copy of V, at this point it doesn't matter, because his body got scrubbed of any mind by the Soulkiller) or Johnny into the brain, possibly by recreating the synaptic map of the brain in the moment it got hit by the program, plus adding the few memories from Mikoshi. However, there is the problem with Relic 2.0... it was rewriting V's brain and body with Johnny's DNA and it succeeded. So when Alt's backdoor (oh, damn, that might come out wrong on so many levels) returns V's mind into the body, once again starting Relic's writing process, the autoimmune disorder caused by this begins anew in a body already ravaged by one. So even if the consciousness of V gets back, he still returns to a body in which the brain is being attacked by the immune system, a sort of extremely violent case of multiple sclerosis (and that is actually interesting, because by 2077, there is an ad for a brand new, very costly treatment for multiple sclerosis, AFAIK by Biotechnica, so V's condition might be cureable, something that writers could have put ingame for a purpose).
And for the philosophy, if V is the real V, if engram is just a copy, that is a question for word's religions... From my point of view, the best way it is descried would be after you save the monk... it doesn't depend on what the body is, but if the consciousness on it is able to experience suffering, it is indeed alive and thus it posesses a soul. And the body is a key.
Sorry for a lenghy post.