Doing shrugs on a standing calf machine has been around for many, many years. It takes the weaker link of the grip (if not using straps) and position of the bar out of the exercise. On occasion your might try doing one side (alternate) at a time to insure strength and muscle balance in the trap area. With the weight resting on the shoulder/traps this exercise becomes more of a Hise Shrug. A great amount of weight can be piled on this movement for good results. No need to do any other shrugging exercise in a workout in this one is done correctly. Good Luck.
PS: Of course if the pads dig into the shoulders than drape a heavy towel(s), baby blanket, etc over the shoulder/trap area. With enought muscle mass on the traps/shoulders there shouldn't be too much of a problem.