My take on this is purely a result of personal experience. I don't think that on long rides where there is not much stopping and starting and you maintain a cadence of about 90-100 rpm, there is probably little difference. However, this does not explain why I quite obviously was in much better shape after I just started adding about 20 miles a week fixed. The only explaination I could come up with is the stopping and starting I do in traffic was more of a workout on my fixed gear than road bike. Instead of gearing down, I essentially had to do leg pressing to get back up to speed.