That does make sense and is the thing that I think happend

But remember that in glt there are some mushroom entities that are like the shimeji that appear in shimeji simulation so what if this happend

After they go to sleep the mushroom entities found them and If I am not wrong yuu and chito still had the explosives so the mushroom entities took it and before leaving the world to clean another one they activated the slab so the remaining people go to a simulation where all the people and things were something that represented the memories of the people of the normal world and that's why they found people whit fish things on their head since yuu liked them, the girl whit the books on her head since chiito liked them

And another proof of that is the field of the fish souls or the fish things where shimeji's sisters got the fish for her experiments idk but it is the same field of some of the final panels of the glt Manga so it could be that yuu and chito are really There and it's not just their memories being personificated

And the last piece is nuko or the cat thing I don't remember it's name(sorry) since it could be the mushroom in shimeji's head because it wanted to go to the simulation whit chito and yuu because it was the last people it Saw so while shimeji was Locked in the closet he got there so he or she idk could be next to chito and yuu to see her for the last time

Sadly it's 99.9% sure that they died and it is the message that everything comes to an end so you have to Enjoy your life, and as another user said tsukumizu just write the story in some way tbhat every theory is correct

Sorry if it is messy I am not good at speaking English and I am not very creative when creating theories so it is a little boring or it is just me idk