The boat Michael takes may or may not be the original ferry.
The ferry doesn't have to be fot a boat at all, and could be a submarine, possibly the Galaga, or an airplane.
It could be where where the helicopter lands in the Sri Lanka video, giving supplies and medicine.
There is an underwater entrance to The Hydra underneath the dock.
Many of the definitions of Pala may apply; The Dharmapala (defender of the law) one is the most appropriate, but the Portuguese "deceive" fits the show itself very well.
This Ferry transports the others around the sonic fence to the dock were the sub was.
A main submarine docks at the island's coast (Maybe the Galaga), at the dock marked PALA Ferry. From here, the recruits go to some form of "Waiting Room" until another Sub surfaces. (Maybe called the Pala). This sub carries people through an underwater channel to the Lake seen on the Cabling map inside the barracks.
This explains why it wasn't a 2 day walk from the Barracks to the beach.
This also explains why the dock Locke went to and the one Sayid found don't match.
A ferry is a boat that moves people short distances. This explains why the dock was called Pala Ferry, as a boat called the Pala would move people around.
Various anagrams of "Pala Ferry" (in regards to the show and the Pearl specifically) are: "A Far Reply", "Pearl Fray", and "Fry A Pearl"