Ethan does not physically require sleep.We know that being imprisoned in Biorite had physical effects on Ethan's body, although, aside from turning his hair black, we don't know what these were. There are a number of points during the game when Ethan seems to be awake in the middle of the night, from the times he sneaks out at night near the beginning of the game to at least one time when you find him awake and staring at a wall (if you talk to him, he'll say that he'll be fine without sleeping).
Save points are justified.As the Fridge Brilliance entry states, the researchers in the biorite facility were clearly experimenting on save crystals. They're also the same colour as biorite and give off a glow. Maybe they're actually crystallized biorite?
Hex tiles are pieces of a being's life energy, soul, or other part of Soul Anatomy.If you do Saraswati's sidequest, you'll find that Hex tiles are the pieces of the sorceror's soul, so the idea that there's some link between the being and the tile isn't entirely unfounded. Also, often, you find a Hex tile after you just killed something, monsters in particular, though there's also Wolfram's tile, which is in the exact place he died, and Tazar's tile, which is also in the exact place he died. Coincidence? I think not. There is, of course, the matter of tiles that are of beings who are still alive, (Tiamat's in particular — where did Barasur get it?) but I don't really have a good theory for those.
The Black King is Valkiris.The Black Mausoleum is not reachable with any physical method of transportation, and it would make sense if it was created by the planet in the same manner as the Gate of Elysium. While the Black King is kind of an evil-themed boss, that is fitting, as he is undead (unlike the four heroes) and seems to have been beyond normal morality during his lifetime That raises the new questions who the Black Rook and Queen were, though...
You fight the Planetary Consciousness for the sake of Alexander and his friends.The main entry notes that there is no explanation for why you fight the Planetary Consciousness, although if you pay attention to the dialogue of the Elysium bosses, it implies that their souls were trapped there by the same being. And even though they did some evil things during the war they still repented (and in some cases even made up for it), so the reason you fight the PC is to get revenge for how it unfairly punished Alexander and co.