When I did my IR training we were obliged to fly everything by hand. After my test, I actually had to teach myself how to use the automatic systems properly, as this had not been covered adequately in the course.
In hindsight, I am not sure this was the correct approach. As others have pointed out, knowing how to make full use of the automatic systems is an important skill. Also, part of my capacity was used up flying the aircraft, instead of gaining situational awareness in the procedures. I wonder whether better results might be obtained during IR training by teaching students to fly procedures on the autopilot initially, and then once they have built up situational awareness, advance on to hand-flying everything.