(Note: I'm most familiar with these terms from the perspective of linguistic typology, i.e. how some languages mark cases using nominative-accusative systems, and others ergative-absolutive.)
I see why this appears confusing, and I agree. But the footnote there seems helpful. If I'm interpreting this correctly, this is because sail is considered to be an active kind of verb, as if the ship is choosing to sail itself, rather than someone sailing the ship. This relates to another concept, of split intransitivity, where (in some languages) some intransitives are marked like ergatives/nominatives and some like absolutives/accusatives (either label works, because the distinction is now semantic, not collapsed, in intransitives), depending on how active the verb is.
A typical example of split intransitivity is an active verb like "jump" vs. a passive verb like "fall". I believe that passage is suggesting that "sail" is more like "jump".
(There's another complex layer here related to metonymy or meronymy, where the "ship" refers to its crew/captain making decisions. If we said "The captain sailed." that would be more obviously an active sentence.)