MC can still become an NPC and leave Eternum, he just can't lose his memory and not be able to see the system like other NPCs, because he is "special", has the help of Calypso and other tools besides the girls , it's not that unrealistic that this could happen, it would still be a way for him to discover the truth about death's interaction with Eternum...
Your theory of him staying in vegetative mode is also not unrealistic, he could stay in a "coma" for some time, even if it's just hours, since he would probably be taken to limbo and there "time" does not exist, he could face anything there for years and also get answers from Idriel before returning to reality without time passing...
This is the exact problem that I mentioned earlier, these small flaws in the story that have not been explained from the beginning until now are what allow all of this to be viable and possible.
However, I started thinking again about my theory n.8 and it increasingly makes more sense and would also be even more interesting and complex to have in the story, it literally fills in all the gaps and would delve deeper into the mysteries of Astral energy even before the interference of "Founder".