Perhaps it is a historical development design fault, like many others in the game.

Perhaps the campaign was written at the time as the 3D designers had not yet finished the subpens, therefore the mission designer placed the subs outside in the external basin. At the time the subpens was finished, there was no more time to correct the starting positions of the subs. SH3 had to hit onto the market by a final divorce of Ubisoft.
You can see this fault also in Kiel. You start outside the subpens in an empty basin, you can hear the farewell music but the nurses and other people stands far away from you in another part of the harbour :rotfl: