My guess is that bunker fuel is (way) worse for other pollutants - sulphur compounds etc, but overall much higher efficiency when used to drive a giant container ship, so much lower CO2 per unit of freight overall.
I'm not sure bunker fuel is worse for other pollutants. There's going to be much more jet fuel. If jet fuel emits 1% as much sulphur but there's 100x as much burned, then it's a wash.
