Page 29: "When a ship is damaged, use the leftmost symbol still uncovered by damage counters in both the Ships Damage and CRew Damage track."
Seems pretty conclusive to me. And the hand symbol spanning both tracks is pretty clear too. It may just be me but i really don't see why there is any confusion here.

FWIW, whilst I've observed that the majority of our ship strikings have been caused by hull damage loss, the number of ships lost to crew damage has been significant (around 1/4), and the likelihood of a ship succumbing to crew loss is (I suppose) rather higher if it has been involved in a boarding - either as a loser in a BA or having won but suffered heavy losses in doing so which sets it up for a fall to gunfire induced casualties later.