I appreciate that you cited a paper, but I think you are overstating. The paper discusses CO2 emissions, which indeed are lower for transport by ship than by trains. But the parent was talking about "environmental damage" from ships that burn the "nastiest, most sulphrous and damaging forms of crude oil", and thus was referring to pollutants other than just CO2.
This report, for instance (I have not read it completely) says "Rail is generally the cleanest mode of transport for most pollutants" and "Maritime shipping is one of the cleanest mode of freight transport, except for PM and specific sulphur oxide (SOx) emissions". While there is lots of emphasis currently on CO2 emissions, other pollutants are also worth considering.
