This is probably dumb as it doesn't affect game play. Just a bit a realism to make you feel like "You are there", to coin a phrase.
Could it be possible to add a gangplank from the sub to the dock? Also when you RTB you will be on the conn and then have to climb down and walk across the gangplank to the dock?
It jsut seems dumb to dock at your base and find yourself already on the dock. Ya gotta get off the boat somehow.