If you warp to a ship that's in mid-warp, where do you end up? At the target ship's destination, current or initial position?
You end up warping to the pilot's current position. Makes perfect sense: if the pilot would warp 100 AU away, you could start warping before he actually reached the destination.
An exception seem to be deadspaces. You will always warp to the beacon in the first room, i.e. if the pilot would warp in and move 100km away from the beacon, you will still warp to it instead of the pilot.