To sum up then, although the sub is a combat vessel, it cannot control an occupied sea zone on its own.
Correct. Subs alone may nearly always be ignored. The only exception is that unaccompanied transports may not conduct an amphibious assault if there are enemy subs in the sea zone.
A german destroyer in the water here, however, would need to be engaged as entering the sea zone would then be a combat move. Do I have this right?