People mean different things whey they talk about emissions. Shipping is particularly dirty because of the low-grade fuel that they've been using. Its very high in sulphur content, and typically contains a higher fraction of heavier compounds that don't burn as well.

So the ships produce more unburned hydrocarbons (smog precursors) and sulphur oxides (acid rain precursors).

So even if the total CO2 emissions are similar, the other toxics are still greatly reduced.