Yeah. The cyberspace is not really explained. But it has to function just like everything else. There's a good and bad side. From my personal take. V going with Alt, and Johnny taking the body. Is the best outcome over all the endings. Nothing directly denies that what the Relic chip is doing. V 2.0 of the chip is 100% taking your mind of the brain, and moving it. So ALT has V. V through the ENTIRE game. Fought Johnny to the end. V will do the same to ALT.You need multiple angles to form an informed answer.
A good example would be the nature of cyberspace in this story. It's simply shown as a hellish place. The digital afterlife in hell. This point of view is never questioned and the player has no chance to look at it with the own... Cortex.
Having a 100% working body. With someone you can trust. And mind ready to recombined later. Is a lot better than the body being in the messed up state in the other endings. Or the dumbest ending of going into Mikoshi. Falling for Arasaka's BS. It's all nice and happy to have money, or be with Panam. But you're dying. You're not dying in ALT. You're trapped. While you have people who can fight to bring you back, in another story.
There's other things that give hints to the truth. When you have characters endlessly try to drill in the fact that ALT is gone. The AI contruct destroyed her. That usually is the writer trying to tell you to NOT think about the potential outs they have in their head. If this AI construct can become all powerful. V could become the same. And take over the AI body.