*snip* Remember, there's a quarantine due to the presence of the blight on Vvardenfell, but I can't really imagine how the empire would go about a quarantine of such a large island. I assume it's not a militaristic blockade. It's probably only a hold on travel between ports of the island and the mainland except for government business (like your prison ship). So once the blight stops I will script-enable ship travel between ports.
You know that idea of the quarantine never makes sense to me - The East Empire Company is obviously shipping goods between Cyrodiil and Vardenfell - importing alcohol and exporting kwama eggs, Bug musk and resources - Vvardenfell receives slaves and I would believe saltrice from House Dres - there are not enough farms on the island to support the population so it would seem logical House Dres is supplying them with food.
Settlers are surely still coming into Vvardenfell despite the blight
Asciene Rane doesn't put up much resistance to transport the player to Mournhold.
So I think you are close to the mark that travel is restricted - but I would think it was for trade, moving the Imperial forces and for the political heavyweights of Vvardenfell to use
I suspect that total travel restriction is completely unpreventable - after all there are all the smugglers on the Bitter Coast who are likely making the short trip across the inner sea to Morrowind mainland to trade Dwemer artifacts and ebony - and would cause starvation and economic ruin of the population which would incite the Dunmer against the Emperor - something he is trying to avoid by sending the player there in the first place.
Sorry for the lore rant - the quarantine just doesn't make sense to me so I think you or other modders putting in travel between Tamriel and Vvardenfell is perfectly legit