Is terrain applied to docking location after Message in a Bottle is triggered? (I assume it would be on a case by case basis whether or not the terrain rules say “touches” vs. “moves over”)
Message in a Bottle is meant to just dock the ship at the island, and not potentially act as another Lost, so the ship should be placed at the island in way so that it doesn’t touch terrain if at all possible. Following the standard placement rules for terrain that should be possible the vast majority of the time. In the rare case you can’t place the ship without it touching terrain (perhaps due to house rules allowing terrain to surround an island or something), ignore the terrain while docking the ship, but then apply it normally as soon as the ship tries to move away.
Is PotC Dead Man’s Chest automatically unloaded to an HI if you are stating not to use it for any gold? (ex: to keep it on your ship and use it at a later time, or it must be unloaded for 0 gold)
Dead Man’s Chest must be unloaded when you dock at home – that part isn’t optional. You only get to decide how many crew to eliminate, and you can choose zero.
Are outriggers considered part of the bow for movement/etc purposes? (Catamarans/canoes/etc)
No.
Can you trigger the Mines UT when a ship already within S starts moving? (regardless of which direction it is going, such as away from the ship with Mines)
You can trigger it as long as some part of the ship is within S during its move action, even if the ship moves away.
Can a ship still use S-Board if Mines causes it to become derelict? Can the same ship still shoot before that last cannon gets eliminated by Mines? For clarity, I assume the wording in the UT “end of her move” means her move action, not move segment?
The Mines damage applies at the end of the move, which puts it after any other abilities and effects that happen as part of the move action, including S-boarding and shooting with a Captain.
Do you skip an eliminated player’s turn with Altar of the Loa if all they have left in play is a fort?
No. That player will count toward the endgame condition because they can’t give move actions, but assuming there are enough other players still going to prevent that, the player with the fort still gets their turn in the normal sequence. If there’s nothing within range of the fort to attack they won’t have anything to do, but that’s not enough to skip them entirely.
Can native canoes redock at a wild island that was S-explored on the first turn of a game to take gold from it as a free action? (I assume yes because they’re given move actions, not explore actions)
Yes. The same applies to a ship that used Hidden Cove too.
If the below theoretically happened: is the flotilla’s movement (straight ahead with the St. Joan) blocked by the tentacle? (knowing that the monster cannot pin the flotilla)
Tentacles (and masts) will not prevent or stop movement if the ship is not pinned.