For all the competitions which end at the end of the the final stage (GC, points, young rider, team, mountains(?)) today's stage ended at the revised finish point, and that's where the times were taken and bonus seconds awarded. At that point there was nothing more for the GC riders to race for, which is why they started cruising. The winner of the stage was decided by who passed the original finish line 2km further on. So it would have been possible for a rider to have won the stage but to have dropped drop down the GC.