Little more work. It looks like the tilemaps and sprites are composed before combining the layers so even though the walls on the gfx layer are behind the eye sprite in the window, the color key transparency on the tile layer overwrites the part of the sprite outside the window tiles.
Yay, this is the main missing feature from the video emulation. A good number of games use it (although Akumajou Dracula is probably the most noticable), too.