Cool people had a transparent desktop so you could see the windows open in the other side of the cube.

Which is a technique some memory athletes use to remember things! They often use spatial cues like mentally placing a piece of information somewhere in a room or town.

Maybe the brain prioritizes things placed in the world over ephemeral things.

I think it's more that the brain has special circuits for remembering things spatially (wether real or invented), and spatial-oriented memory "hacks" are just piggybacking on those dedicated circuits. It's like how GPUs were designed for games but it turns out they can work great for other tasks like machine learning too, if we massage the problem a bit.

Hijacking spatial memory like that is really useful.

I used to use 6 desktops (in Enlightenment 0.16) in a 3x2 grid, which I could slide between by throwing the mouse to the window edge.

The Compiz cube made the transition a bit fancier, but only made sense when the desktops were arranged in a line, and anything other than 4 didn't work as nicely.