When such ditch or drain crosses any railroad track or right-of-way, it shall be located at the place of the natural waterway across the right-of-way, unless the railroad company has provided another place in the construction of its roadbed for flow of the water, or unless another place for so crossing its right-of-way is agreed upon by the railroad company; and if located at the place provided by or agreed upon by the railroad company, such company shall be estopped from afterwards objecting to such location on the ground that it is not the place of the natural waterway.