Not only is the leg extension bad at the top of the movement, but even more so at the bottom. For most people the bottom of the leg extension places a weighted over-stretch on the patella because of the position of the pad and the seat. Notice how when you hook yourself into the machine you have to be sitting up before you get into the reclined position? You can't be reclining in that machine to do anything safely except relax with your leg propped up on the pads.
Also, the GHR on a GHD is a compound movement because it incorporates back, hip and knee flexion. The hamstring raise is a single joint movement. Also the GHD situp is like the anterior chain equivalent of a GHR. At full ROM it does place the hip in complete extension (hyperextension for some) and the knee in flexion. From there it completely closes both joints.