Yes, they have the same insertion, but they have different origins and therefore different functions. Vastus medialis, intermedius and lateralis originate on the femur, whereas the rectus femoris originates on what I think you Americans call the anterior superior iliac spine (ASIS). This means that the "vasti" can only extend the knee, whereas the rectus femoris can extend the knee AND flex the hip (great way to make it stand out when posing, try it).
Since how well you stretch a muscle apparently affects how recruit it, exercises like sissy squat variations (where the RF gets very stretched) can hit it in a way that normal squats can not.
Foot positioning is another way to tweak the exercise for your needs.
Hope that made sense.