When Pala Ferry appears on the show, the water surrounding it is very calm. This suggests that its location is in protected water, away from the crashing waves of the ocean. The atoll would provide such a barrier from the ocean’s waves, so it’s logical to assume that Pala Ferry is located in its vicinity. The Barracks orientation video seems to confirm this, because it mentions that the ferry runs to Hydra Island three times a day. If the Hydra is located in the atoll, it would make perfect sense for the ferry to be nearby.

However, in the Pearl orientation video, DHARMA members are instructed to report to Pala Ferry following their shift in order to be transported back to the Barracks. The Pearl is farther from the coastline than any other station, not to mention the fact that there are mountains between it and the western coast. The journey to Pala Ferry from the Pearl is about the same distance as simply returning to the Barracks over land. It makes very little sense to travel that far over land, only to take a ferry all the way around the northwestern quarter of The Island, especially considering that the Initiative had vans and jeeps, and a system of roads to the various stations.

Perhaps, because of the secretive nature of the Pearl experiment, DHARMA members who were stationed there were sent on a circuitous route to and from the Barracks in order to make it difficult to recall its location. That’s the best explanation I can come up with, anyway.