Assuming that the theory we get introduced to in the library scene (the one stating that the world is just a computer simulation containing the souls of all the people of the previous world, which was devastated by a plague and then a war, then blasted off into space) is true, which seems likely considering in the final chapter we see the computer floating around in space, then this would line up perfectly with the story of GLT. In that world we see that there are very few humans left, yet no mountains of corpses like you would expect if everyone had just died. Additionally, in the chapter of GLT where the girls find the rocket, we see that one of the previous rockets is currently chilling around in deep space, potentially the one with the supercomputer that runs the simulation in Shimeji Simulation. Finally, at the end of GLT the two MCs fall asleep in the snow next to the strange black stone with computer code embedded in it, but then we see them having seemingly disappeared, leaving all their gear behind but having wiped the snow off a lot more of the black rock, revealing more machine code on it. Then, we see them riding the train in Shimeji Simulation, suggesting that they too are in the supercomputer. Thus, my guess would be that the black stone was a transmitter (hence it being the only structure on the top of the highest point of the city) that, once they uncovered it, transmitted their souls to the supercomputer, putting them in it along with the rest of humanity, hence why we see their gear left behind but no corpses.
I could of course be very wrong about this, as maybe there are some important things I missed. I do very much want the two MCs of GLT to be still alive, I think it would be a fitting reward for their journey through such a desolate, hopeless wasteland to be able to live in a world of nearly pure imagination with each other.
