HoD is a rank. Anyone with the rank of HoD is referred to as HoD regardless of whether they're currently in command of a ship. When the HoD regularly assigned to a ship is away and someone else is commanding, that person is the ra'wI' and may be referred to that way or by their actual rank, whatever it may be. 

The phrase in KGT exemplifying the idiom to'waQ yIv, used for "take some time to consider a matter" ({HoD QaQbe' ghaH; reH to'waQ yIv} "He/she is not a good captain; he/she always chews ligament"), implies that the speaker is thinking of the HoD's role as commander of a ship (whether currently occupying that position or not) rather than thinking about rank. It might have been clearer had the example phrase used ra'wI' (or even yaS) rather than HoD.