Why not use the pico-PSU in the ATX case? Just zip-tie the power brick where the ATX PSU would otherwise have gone. http://www.silentpcreview.com/article947-page3.html
Why do mini-ITX cases have to be on a desk anyway? It's just a matter of desk design IMO. For example, at my local bank I see them using Dell slim mini-towers on small shelves under the desks (not big enough to fit an ATX mid-tower). Could also bolt a small enough mini-ITX case to the back of a monitor.
Yeah it's an interesting problem. Custom furniture is the ultimate solution, but then the furniture becomes part of the system/design/cost.
MIni-ITX on the floor will get kicked, scuffed by vacuum cleaners, too low for access, etc. On the desk, it seems in-your-face however small, and brings the mess of wires on your desk as well.
A floor-rolling ATX is convenient, rolls out for service & house cleaning, ideal height, but I can see that ATX cases & PSUs are basically outdated formats.
floor-rolling = viewtopic.php?f=14&t=66864