After a long night of sleep and some playing around, I discovered that as wungasaurus said in noggit you can see the Wintergrasp models but they use a fake .wmo to create the collision. It can be seen in noggit but not in the game. That's why if they spawn a normal Game object on the exact same spot it fakes the vmaps/mmaps.
How can this help me? I think it is possible to put the boat in noggit and create vmaps/mmaps for it. Then remove it from the map and only spawn it in the phase like I have now. This makes so the server knows that there is a boat there but not the player. The only downside of this might be that if a player outside of the phase (will only be water next to a beach) if they swim while an npc are attacking them and swim over the place the boat is on another phase the npc will act like crazy. Is this a stupid idea? or the easiest one?
I know that all .wmo are loaded from the map but is there really that less support on the serverside to spawn .wmo with type 14?