I have thought about doing one like this, except I would turn them around so the doors are on the backside of the shop and therefore not visible. Use the bottom ones for lockable storage for skid steer, excavator, tractor, truck, etc etc. My plan for one top one would be shelving for parts storage, heavy stuff I can sit in from outside with the skid steer, but I would have a catwalk between the two inside for access. The other upstairs unit would have the mill, lathe, drill press, CNC plasma table, and other stuff that doesn't get used often to keep it out of the way.
I would build as a 30x40 shop space (between the containers) and run a large I beam across in the center to use for lifting in the shop (engines, etc).
The other reason I have though about doing this is I can get lockable storage quick. I have means of sitting the containers in place without renting equipment so I don't have to sit them all at once either. The biggest issue is getting it engineered, I have talked with an engineer but he has not given me a price yet.