They are probably plotting the HPG pulse hours ahead of the scheduled transmissions. In fact, since they know where they will be, and they know where the other ground location ill be, they might even be plotting the burst's transmission coordinates days, weeks, or even months ahead of time.
Also when they say 'exactly targeting on the ship' it's not precisely true as far as I can tell. It just has to get to the exact hex the ship is in. The target is about 18 km wide. Still tiny when you are talking about interstellar distances, but much bigger than a ship's HPG dish.