The FCTM says: The AT Arm mode is normally not recommended because its function can be confusing. The primary feature the AT Arm mode provides is minimum speed protection in the event the airplane slows to minimum manoeuvring speed. Other features normally associated with the AT such as gust protection are not provided. Some malfunctions that affect manoeuvring speeds cause the AT to maintain a speed above approach speed.
In the simulator when some pilots hand fly but with the AT engaged, it is most annoying (to the passengers down the back as well) to see and hear the continual pitch changes and engine noise changes as the pilot tries to maintain level flight for example. If his manual flight is rough due lack of practice or more likely lack of flying ability then the AT works like a drovers dog - always moving. It means sloppy flying.
Boeing test pilots must have researched the manual flight/AT Arm combination and decided for technical reasons that manual flight means AT off except under certain periods of flight. But check pilots often have a personal preference and teach that preference as gospel rather than accept the Boeing advice. Personally I prefer to stick with the advice of the manufacturer. Particularly in a court of law.