Frankly, the "whole series takes place in an abandoned video game" makes absolutely no sense no matter how you slice it. Every single way you could think of to make it work is just absurd, whether it be the players somehow staying being on life support just via a headset, OR via their mind being scanned in, it doesn't make any sense. Aside from the amount of technical advancement that'd require - likely hundreds of years worth - imagine how much power that would eat up. This would be a global project from the richest companies in the world produced exclusively for the mega-elite, not some random beat up 90s company working out of a parking lot or whatever. It's a patently absurd premise. Maybe if the big twist was that the game was made in the 5990s, rather than the 1990s, it could make some sense, but I somehow feel like that's not the case.

This is fine, though, because it's the premise the series is built on, and the whys or hows of it all aren't elaborated on. It'd be a problem if it was like, a twist at the end of the series, but frankly I think thinking about the practicality of it all and trying to justify SOMA theory around the fact it makes a completely impossible thing slightly less completely impossible (but still impossible) is silly.

You're not wrong to be engaging with the series on a logical, practical level, but I wouldn't waste that time and energy on thinking about the setup.