The next scene after this one does have skulls and such in it... This place was meant to be a vast, empty, directionless desert. There's a puzzle which involves navigating it.

No - This is literally the whole screen at this point of the game. It's a one screen navigation puzzle. There's an object on the screen that changes location to show you which way to go - like the typical "magical forest" puzzle you see in most RPGs.

There's a proper dungeon beyond this which is mapped normally.

I hated Yume Nikki's landscapes...