After the work specified in §§ 56-366.1 and 56-366.3 regarding underpasses and overpasses has been done, the maintenance, including drainage, of any underpass hereafter so constructed, except the pavement thereof, shall be the sole responsibility of the railroad company and the maintenance of any overpass hereafter so constructed shall be the sole responsibility of the Department of Transportation or the public road authority; provided, that the railroad company shall not be responsible for any damage to an underpass caused by operations on the highway, and the Department of Transportation or the public road authority shall not be responsible for any damage to an overpass caused by the operations of the railroad company; and further provided, that the provisions herein as to maintenance of overpasses and underpasses shall also be construed as applicable in the case of those structures previously built on the primary system under agreement between the railroad company and the Department of Transportation or the public road authority; and further provided that the provisions herein as to maintenance by a railroad company shall not be applicable in the case of any underpass hereafter constructed without eliminating a crossing of a railroad and a highway grade, but the maintenance of such structures, including highway drainage and pavement therefor, shall be the sole responsibility of the Department of Transportation or the public road authority.