It is all about the back – how back “behave” during short and long lunge.
During long lunge back tend to be “in place”, during the short lunge we are forced to bend forward quite far, bringing lower back very strongly into exercise.
Full LONG LUNCH are exercises for developing all four heads of the quadriceps.
The SHORT LUNGES targeting more the outside sweep of the quadriceps.
Yes, I think the short lunge would be harmful to the patellofemoral joint, and the quad would be the most responsive muscle used whereas a long lunge would integrate the hamstrings/gluteal muscles along with the quads and the knee and ankle joints would be lined up in an angle that would provide more support throughout the movement.