No railroad company, or person owning, controlling, or operating a railroad in whole or in part within this state, shall charge or receive any greater compensation in the aggregate for the transportation of freight of like kind, for a shorter than for a longer distance over the same line or route in the same direction, the shorter being included within the longer distance, or charge any greater compensation as a through route than the aggregate of the intermediate rates, within the state. This section does not authorize any company or person within the terms of this section to charge or receive as great compensation for a shorter as for a longer distance. Upon application to the public utilities commission, such company or person may in special cases, after investigation, be authorized by the commission to charge less for a longer than for shorter distances for transportation of freight of like kind, and the commission may prescribe the extent to which such designated company or person may be relieved from the operation of this section.