A new option for underway replenishment (UNREP/RAS) of ships is the Ampelmann self stabilising platform. This has computer controlled jacks which compensate for the motion of the ship. This could be used to transfer crew and cargo from a ship to a Collins class submarine, as well as other vessels.
It may be possible to apply the same technology to the jack supported ramps fitted to the the Australian designed Joint High Speed Vessels (JHSV) being built for the US navy. This would allow the ships to transfer cargo, vehicles and personnel at sea while underway. For safety reasons it might be prudent to use remote controlled fork lift trucks for most cargo transfer.