The Isle of Man folk have posted sector-by-sector results from the 2013 and they give a little bit of insight into why the race ended as it did.
On almost every sector Michael Rutter took the sector a few seconds slower than did John McGuinness. After the Bungalow sector that changed, and Rutter took the next two sectors faster.
This matches McGuinness' report that Rutter disappeared off into the distance after the Bungalow. It also matches Mark Miller's description of the team strategy.
Meaning, that Rutter was holding back on the juice until the end, to make a sprint and go for the win.