Real good points.
When reading the outline/interview on SHIV I took the liberty to think that setting watches would also involve where the men would be during different times of their watch. Ex. lookouts most times where the ones - when the order to dive came - went directly from the periscope sheers to the control room and the fore and aft dive planes. The OOD - though the last to leave the bridge - went to his assigned station ex. the diving officer - if the OOD - would go directly to his station in the control room or the Officer whos funtion was the TDC, would go to the Conning Tower if the dive involved an attack.
I hope that this is part of the watch set. In SHIII too much is involved in getting the stations maned, and as has been noted previously, some functions happen without men even at the station.
Though US Boats were bigger than U-Boats and more men manned stations - the same procedures were needed to "drive" the boat either on the surface or submerged - during normal cruising or during an attack. The Captain never had to order men to man the planes or the dive station etc. This was automatic per each mans assigned function on the sub.
Hopefully this is incompassed in the watch setting feature the Dev Team has said would be part of the sim.
Happy Hunting