He's talking about pixel placement when making tiles, not how to use tiles.
OP, the only cases in your pictures where I'm 100% sure it was done through some texture or algorithm are the walls (e.g the desert ones, mado's room, the wall where you get the ghost kerchief effect). Those more than likely had some "noise" added onto them and then filtered to get the resulting "texture" feeling, then one side got darkened to get a 3D feeling.
The floor wood boards and the book shelf on Mado's room, as the bricks in the skygarden are more than likely done by hand. Just practice a little.
I have my doubts about the sand in the desert. It seems done by hand but don't quote me on that.