Do you have to "land" it in front of a dock? Or does it just land wherever?
What I did was take the solid river tile (the middle one), add the Landing property to it while removing the Obscures Half property, and placed it right in front of the harbor so it would appear like you have to park it at the dock.
If it looks right, I might make the tiles shorelines (or at least some of them) be parkable spots as well. I can't remember whether or not if that would make it closer to how the NES FF's Sea-Ship acted, but it would certainly open up some exploration possibilities!
I also found that if you save the game while riding a vehicle, loading said save causes some wonky effects, such as:
1) AIRSHIP = when the game loads, airship is set to either it's normal speed or some faster speed. The airship's animation frames go at normal marching speed, and the Mode7 effect is inactive. Some graphical glitches when landing, but everything is normal once you re-board it.
2) HOVERCRAFT = when the game loads, hovercraft will be at walking speed, and animation frames seem normal. Landing and re-boarding the hovercraft fixes the effect.
Hmm, I wish there were a way to just block access to the menu while on a vehicle, being that would keep players from experiencing that. Or if I had a grasp of ASM, I'd rig the menu button to transfer to the deck of a given vehicle like FF6 did for airships.
I know I found the place where the game turns off encounters for the hovercraft (and airships, and everything else) once, I'm sure I could find it again and manipulate it.
Whoa, that's incredible! If you happen to find that place again let me know, as I'd definitely enjoy some on-vehicle monster encounters!
