--Snip. Not that you don't make good points here, but I'm only responding to the second part.--
I understand, the reason that I think this question is important to hash out is I personally don't think saying "Actually, V doesn't only have 6 months in the Panam ending" isn't a good ending, either, unless you're ok with V2 living instead of V.
If V2 doesn't know she's V2, and Panam doesn't know she's V2, and literally nobody besides Alt, who V will never meet again, knows she's V2, then I think no, it doesn't matter at all. As far as V2 knows, she's just V.
Even if she is aware that she's an Engram of her former self, as long as she treats Johnny's Engram as a full person, I see no reason why Engram V would feel any different about herself, and THAT'S what I want. I want V to find peace. I want all the choices I made for her to lead her down a path towards life, not death. It doesn't have to be a flawless, perfect life. Say she gets awful headaches every few days or something, idc. Simply being rewarded for everything she went through long enough to live out her life to its natural conclusion is enough for me. She's a merc, she'll probably catch a bullet in 6 months anyway, and I'm fine with that. I want her to live until then, because she did all the things she needed to do to survive, and to tell her "nope too bad, you die now" is not good enough.
I mean, CDPR made this into a survival story. It didn't start that way, and wasn't sold that way. They MADE it about survival. Well guess what? Survival stories where the hero doesn't survive have been rare since the dawn of the printing press (until recent RPGs, apparently) for good reason. Nobody wants them.
Back to your question, I guess my point here is that if V2 doesn't feel like has she lost anything by becoming an Engram of herself, then did she really lose anything? She has already replaced her eyes and her hand with Cyberware versions. My own V has replaced just about everything with Cyberware, all slots filled, but even if you want to keep your V somewhat "pure" you can't remove the Cyberware eyes. To say that an V2 is not V is like saying that V is blind once she has her Cyberware eyes. V2, since she is a complete copy of her psyche, is no less V than her organic brain version was.
If anything, she's V2 in the sense that she's a better, upgraded version of her former self. A nanite brain could self-repair if she gets shot in the head again. It would be immune to degenerative diseases like Altzeimers or Dimentia. In fact, one of the news broadcasts in the game on the TVs states that MLS is one of the few conditions that is not treatable with Cyberware. Yet, with a nanite brain and an additional nanite spinal chord, V would be immune to MLS, making her the only person on earth with such immunity.
So yes, I'm perfectly fine with V2 living, because V2 is just V with another, advanced piece of Cyberware, that just happens to also save her from death. V2 is absolutely still V. She's not V1, but she is V. I'm not okay with neither of them surviving, though.
Also, I haven't played the Panam ending, but my understanding is she only has 6 months to live that way, too. That's my whole issue, basically. We have choices to make, but they don't matter. If you're just nice to Johnny, you unlock the secret ending and that also gives V six months. No matter which angle you try to work it from, V dies.
Personally, I'd like what I suggested before. Find Johnny's arm and trick the Relic into not killing V in the first place. It's a clean answer to an otherwise very murky problem.