You are absolutely right. The odometer does not go by the GPS speed (not all models are even equipped with GPS). The only way the odometer "knows" the distance is by the number of wheel revolutions and presumed diameter of the tires. Since over the life of the tires their diameter only goes one...
There may be a more "sinister" explanation for speedometers in Leaf always running high. A vehicle without GPS "calculates" the speed and hence the distance from wheels revolutions per second and tires diameter. By programming the speedometer to read high (mine is also high by approx. 8 percent)...