Okay let's see what i saw ingame:
- Arasaka Ads: chip saves the soul and yourself. (Still you find emails - e.g. on the Laptop you find with Hanako near one end that engrams are a failing and not the complete thing).
- In the Hotel room scene, Hellman: "The Biochip is what's unique, not Silverhands engram... The previous version of the chip was only used to to communicate with pre-saved engrams." - V: "And it was rare as fuck and cost a fortune, yeah." - Hellman: "This ones rarer. Meant to install and activate the engram in a new body."
- With Alt at the Voodoo Boys: - V: "So... you'll save my life but flatline me along the way?" - Alt: "Your consciousness, neural engrams, will be recorded as data. The rest will cease to exist." - V: "The rest?" - Alt: "The soul. I did not grant the program its name, but Soulkiller does precisely what it promises to do." - Johnny: "Christ i don't want listen to this bullshit. V just hops back into her body, right? Nothin' changes." - Alt: "Everything changes. You know this well."
- Engram Jackie - Not the real deal either, right?
- Johnny Silverhand - Jumps from him being him and him not being him, as far as i remember Johnny.
Anything i'm missing yet, that's actually saying that Soulkiller 2.0 is different from what Alt tells us? Or Arasakas internal emails?
As Alt says herself, She didn't name soulkiller, that the "soul" dies is her interpretation because it happened to her (and she was disconnected too early by Johnny).
Arasaka isn't the creator of soulkiller, Alt is so she'd know how to handle the engrams the best, she's so good in fact she can edit them in real time then plop them back into a body. She also originally designed it to more easily move around the net, it was never meant to kill netrunners, That's Arasaka's addition.
Jackies engram was made after his death, it is incomplete.
Johnny is still Johnny, even comes with being an "unreliable narrator" like most real human beings.
Like Hellman says, the relics ability to overwrite people is bleeding edge, meaning the engrams are already fully conscious and just need a biological body to function properly.