Diving only takes you to the NPC that starts the tale for obvious reasons. It would be weird if it just teleported you into the Sea of the Damned without context. So the portals are still needed.
And if the portals were just replaced with diving, it would be hard to make it work with the cutscenes. Castaway clearly opens a portal but if we remove the archways, it will just be a confusing and anticlimactic move.
The Pirate Lord opening a portal would be very awkward too as he would point to nowhere with Kate looking surprised at said nowhere.