But that is why you spend hours in the cardboard bomber with your sim buddy before you go near the sim. The FMS isn't touched for the reason you stated. The extra time is jet handling without the autopilot. This teaches you multitask and work with the other crew. After all as you know, some emergencies call for the AP to be out while you deal with the problem. I agree that you loose your edge very quickly and it is a lot of money, but
if you want the best chance of passing a sim check.....