Ball of the foot over the spindle. That's how I ride the commuter, too (platform pedals, no clips). It hurts my knees even thinking about putting my arch over the spindle. Maybe that's because I'm an overpronator and it's not so easy to correct for that while cycling??

ETA Post a link to that article, but it doesn't really make sense to me. Your arch isn't made to touch the ground when you walk or run - why should it touch the pedal when you ride?