1- The APU flap lever is just below the fuselage and smoke from the running engines can go in, we processed by the APU and then thrown inside the cabin. The smoke itself is uncomfortable and many people don't like it. If the smoke is dense, it can trigger a false smoke perception on the passenger cabin with all it goes, and might end up with an evacuation drill.
the APU bleed is turned on to avoid another pack on/off cycle, to continue providing fresh air to the cabin when the engine bleed is stopped and to assist if a tailpipe fire event happens.
2- Correct, but high flow is not dependant on how many packs you have on, but it is the system which will provide high air flow to one or both packs with a single engine source or APU at ground.
3- I don't recall any value for negative pressure values, though there might be one.
4- Operation in manual mode is slow. As you said, the control in manual mode is less precise, it operates under DC motor opposed to an AC source, and the readings might be slow and difficult to read, plus some people might get impatient and keep ticking on the selector without waiting enough time, hence why there is that ample margin.
4b- The answer is in the FCOM.