I too read the article but the #3 ranking for pilots pertains only to the incident of death caused by an accident vs injury. This seems correct as sudden stops by aircraft are of course more violent than those of a boat/bus etc. You will note when the stats are broken down in fatal accidents per 100,000 worker years, pilots/aircrew do not appear on the chart.
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Workers who died from accidents at work Fatal accident rate per 100 000 worker-years (95% CI)
Fishermen* 454 103·1 (87·5-118·7)
Merchant seafarers* 507 51·6 (38·7-64·5)
Energy and water supply 700 10·0 (6·7-13·9)
industries†‡
Agriculture, forestry, and 737 8·8 (8·2-9·5)
fishing†§
Construction 2404 8·4 (7·6-10·3)
Manufacturing 2264 2·2 (1·9-2·5)
Service industries† 1619 0·7 (0·6-0·7)
All workers¶ 9543 2·0 (1·7-2·2)