Well maybe because AT primary role is to transport. Subs main role is surprise attack (in theory). Transport option is somehow a bonus like for helicopters in DS, and I know that in practice subs are just stealth transports rarely used for attacks but that doesn't mean they should be underwater transport for 4-5 units with 7 or 9 attack and stealth. If we go with capacity II why not make them benefit from Safer Transportation's +3 HP?