I believe this is not the end for them. The black stone is some sort of machine. When Yu asks "What's that?", Chi says "Seems like some black stone." and then Yu replies with "Is it just a stone, or....". I think the author is implying that the black stone is not exactly what it seems. Even in the last panel you can see to left strange markings starts to appear on the black surface similar to machine code. The extra chapter takes place right after this as you can see Chi and Yu sleeping and the shadows are at exactly the same place. Notice not much of the black stone is revealed currently. Then the camera pans out, we some other parts of the city and then when we come back, a large part of the stone is uncovered and a machine code pattern is glowing. THEY ARE STILL ALIVE.
none of that "they never woke up" bs.
i rest my case.