The shorter fan is for the motors (like the one the SC679 comes with) that have brushes on the bottom closest to the fan. The motor bearing plate has to be thicker, so the fan has to be shorter as a result.
There isn't a dimensional difference in the bases (in the fan chamber/motor mounting area) between models, so you can indeed take the larger 7 amp "pancake" motor with the taller fan and use it in place of the original motor. You just can't take a taller fan and put it on the smaller motor.