Why not unassemble the cylinders and re-assemble into rectangle chasis? Im sure that would give you a more dense layout.. Sure it would void warranty and resale value.. but do you really care?
Electrically, everything's built around a round "central" PCB using a custom interconnect. You're not going to be able to reassemble the thing into a rectangle and still get a functioning machine (not without tons of custom design work, at least).
See https://www.ifixit.com/Teardown/Mac+Pro+Late+2013+Teardown/2...
Since we were able to get the Pros to the point where they effectively occupy 1U, there wasn't really any incentive to doing a disassembly style integration. Maybe if Apple announces the next Mac Pro comes as a triangle.
To your other point about the warranty and re-sale: we do care, but only a little. I budget machines to have a usable lifespan of 3 years, but the reality is that Apple hardware historically has significant value on the used market for much longer than that. So if we can recoup $500-1000 per machine after 3 years of service, that would be great.