Actually according to my rather rudimentary mapping, the finish line being slightly forward of previous years and the route taking you up Horse Guards Road rather than Whitehall, only reduced the total distance by about 250 metres.
The main cause of mileage loss is still the tunnels - if when your device loses the GPS satellites it assumes you have stopped riding and just magically teleported to the other side (like my current Edge 520), then you can lose up to about 1.25 miles across all the tunnelled sections. However if it assumes you carried on riding but went in a straight line until it sees the satellites again (like my old Edge 500), then you only lose just over half a mile, most of which comes from the Limehouse Link tunnel, as that has the most bends.