Spoilers ahead:
So I went through the expedition quest, went to meet the captain of the pirates, and made the arrangements to not only return the professor but to allow access through their turf as well as that of some laborers (Not sure why but it seemed important).
So I go exploring around port-Ceto's walls (since the front entrance is closed), and find it quite nice to get on land and explore the outskirts, the pirates don't go aggressive though they do say things like 'Get a move on' and the like.
Then I turn the corner and go around G-1, and the pirates immediately turn hostile and I have to revert to a previous save... This also appears to be a place that the ferryman docks.
Am I not allowed to go into this area? Period? Unless it's a bug... I hope it's a bug.