I've talked far more than I want to about Soulkiller's implied effects, for this particular post all that matters is that Alt *is* unambiguous about the fact that using Soulkiller to "save" yourself has some kind of dire consequences.
I think she is quite clear the transfer process isn't going to yield a 1 to 1 duplicate. Some of the content is going to get lost in the process. However, I think her comments on the significance of that lost content are largely based on her own perception (aka, it's called Soulkiller because the soul doesn't make the trip <-- Alt's personal rationalization).
To me it seems more accurate to say it constitutes a loss of some part of V if they choose to go through with it. As an arbitrary value, 70% of V gets transferred. 30% goes poof. Does this mean V is dead, gone or ceases to exist completely? I don't think so myself. If 70% of V makes the trip then 70% of V still exists. Yeah, the new V will be different but different and gone are not the same.
Then you can't express concern about that, move through the rest of the game as if it's a perfect solution, and then basically get gaslighted about the whole conversation when the only reference in the ending is "Hey you didn't ask if I wanted to use Soulkiller".
Well, I think it's implied V accepts the risks based on the previous decision to pursue it.
That's where the game arguably screws the pooch in many areas. A choice is made and various implications for what the character believes or thinks beyond that choice get tacked onto it. To me, for an RPG, that's a huge no-no. The player should
never make choice A and have the game extrapolate it out to choice B. If choice A and B exist the player should be given ownership over both of them.
The real tragedy is I'd bet the writers would agree. I suspect they wanted to go further with it and flesh things out more to split a number of choices available to the player up into individual decisions. It was constructed as is because an extra year of development time didn't make the cut.