I use flat pedals to commute and I find I move my feet to different positions depending on speed, grade, fatigue and probably random whim. Right now I have a sore calf due to a running injury, and it feels a lot more comfortable on uphill sections when I've dropped to my lowest gear, to place the pedal under my arch to lessen the strain on my calf. When using spds or other foot retention systems, you don't have that flexibility, so you have to find a compromise position that works reasonably well for all riding conditions.