In my own kitchen and in some bathrooms (obviously after discussing with the client) I've done recently I've done as noseall suggests, stopping the edge of the board either side of the pipework. Then, rather than filling the void, I've simply tiled over the recess (or in other peoples bathrooms I've left it for the bathroom fitter / tiler to tile over).
That way there's no need to worry about cracking if the pipes are heating and cooling. It also gives easier access in the event that the pipes should need to be accessed at any point in the future.
Regards
Fred