In reality here's how it works:
The boat leaves freeport. Players zone. They appear on an identical boat that is stationary, giving the illusion that it has stopped. Of course it never moves and is always at the zone in point.
The "cruiser" comes along. This is the one that actually moves in the zone, and after boarding, it takes the players across ocean of tears to the zone out point. They zone in at qeynos, on another stationary boat (always at the zone in point) that is identical to the boat they were on. So, again it seems to have stopped. The shuttle pulls along side (the boat that actually moves in this zone) and takes them to the docks.
Like I said... we cheated
