It looks like the creator of Magnasanti optimized his solution by hand using pencil and paper, first finding modular arrangements that worked well, then assembling them in a predetermined overall design ("inspired by the Wheel of Life and Death"), which makes this more of an art project than optimization exercise. I wouldn't be surprised if there were still better solutions that sacrifice, for example, aesthetics or regularity.
http://www.donhopkins.com/home/micropolis/
http://code.google.com/p/micropolis/
It looks like the creator of Magnasanti optimized his solution by hand using pencil and paper, first finding modular arrangements that worked well, then assembling them in a predetermined overall design ("inspired by the Wheel of Life and Death"), which makes this more of an art project than optimization exercise. I wouldn't be surprised if there were still better solutions that sacrifice, for example, aesthetics or regularity.