Re: two or zero are the only options
Yes there are many times pilots will just override autopilot. The most common being that ATC ask us to do something that we know none of the Autopilots can handle.
Also, note that a plane doesn't have one autopilot that you turn on and it does all parts of flying the plane. An aircraft has multiple different autopilots that each do different tasks, part of the role of the pilot is selecting the right auto pilot for each phase of flight, and that often has to change to cope with differences between expectations on the ground and reality in the air (weather, other traffic, idiots with drones etc)