Alt openly says there's no 100% copy - she will put a copy on an engram, kill Vs actual conciousness, then reupload the copy and within that the final conciousness will have lost parts of itself (the soul). She openly states Soulkiller will kill the Soul, that's why she named it that way. It greatly resonates with the depiciton of Arasaka advertising the Relic as Soul saver.
But yeah we can always argue about who knows best what happens to the soul with soulkiller or what is meant by soul really...
But i think that whole Soulkiller concept witht he specific lines, without opening acceptance paths for V, is the big failure here. If you read up on Alt on the old wiki, it doesn't sound as if she no longer was the original person (though i completly confess i've never read the PnP stories). And leaving it that way and not having the 6 months timeframe also would have been a better way.
The way it's written is you can't come to terms with anything and each and every way you go the "GM" seem to go: "Yeah you think that's good but actually, see how that's bad. But maybe if you then go there, hehe nah still bad... but over there... ". And i can't discern a message or reason in that exactly, other than possibly life and the writers are bitches (no actual insult for the writers intended)?
But i'm likely a dolt.. so yeah.
Still there might come some DLC adressing things, branding Alt as a lying AI or something. We'll see.
Otherwise kudos to the people trying to find their path to terms with a story that was unfulfilling for them, no matter if i personally disagree with your reasonnings