Since we are in the land of spoilers I will avoid putting anything into spoiler tags.
It's silly accepting Relic can change DNA of V's body and make him die in 6 months because of "different" engram/soul and then saying Arasaka can't provide you a new body. If the Relic has such capabilities then shouldn't it be very easy to reverse-engineer the process and replicate it for new body and possibly allow for immortality regardless of this limitation? Why putting this problem in the story anyway?
Another thing is how you approach engrams / souls. Personally I treat Yorinobu as brainwashed with Saburo memories. One of the issues Arasaka encountered with Soulkiller 2.0 was high sucide rate. I think if true immortality would be possible instead of conditioning with the recorded memories then I think people would at some point decide to kill themselves or refuse to be reborn or soulkilled. It's a spiritual dilemna if one believes in a soul or not. It's a shame this game copies Altered Carbon but doesn't ask the questions itself nor doesn't provide different answers through ingame characters. V at one point throws out of his hat a question to Johnny asking him if he believes in god in Sinnerman quest, Silverhand brushes it off with his signature "fuck, please kill me (don't make me answer)". Also the game is afraid to say if Johnny is real or becomes real by changing V's mind or is merely a virus AI in V's implants designed to fry his brain and hijack the body with the recorded memories. Game is leaving the interpretation for the player who can treat Johnny in those two different ways. Guess it's the only true relationship since Johnny can admit that he is real/fake depending on your dialog options... But that doesn't change the endings narrative.
I chose the Arasaka ending since that is the most logical and safe bet. Your other options are to trust rogue AI which consumed Alt Cunningham and assault the place. Also it's kinda stupid Victor leaves gun besides pills and Misty doesn't react when you put it beside her but then both are bitter if you kill yourself. I think it would be better if V was left alone on his way to his apartment and have to make a choice in front of the mirror with the gun placed on a sink or something.
Also it's cliche your apartment has a view on AV pad of V's mansion from The Sun ending.
The Engram is just a copy of memories. Is that enough for a person to 'live'? Or 'be'? Alt says it best, Johnny is Data now, code. She can read him as easily as a programmer can read their screen. V becomes data, and is flushed back into his rotting body.
They dealt with this in SOMA, too. You could have two copies of the same person about. One in storage, one running around, or two people running around. It's obviously not one person, and I am a Materialist, so sure, copying memories will make a person, but it's a copy. The nanosecond they are cognizant, there is divergence, two new people, from the same root, sure, but differing. But we're not mentally prepared for that, so obviously, we must be the original, right? After all, we didn't experience death, one moment we're in a chair, the next, in a new environment.
V died, the Relic did some emergency nanorepair to keep him alive, but that included altering his body to be Johnny. (Good thing Biometrics don't matter in this game?) All Arasaka had to do was basically stem-cell clone V a new body or brain, or reconstruct something, or allow for the Engram to control a meat body via some special Man-Machine Interface. But eh.