Michael, you're absolutely spot on about my unclear statement. Sorry!

I was speculating that maybe the line that Lighter thinks he remembers hearing in 1967, "What shall we do with the captain's daughter?", may have been authentic to the earlier, oral tradition. If so, then that would resolve the issue of how the phrase "captain's daughter" got attached to the song, and save us from two of the other sticky possibilities being considered, namely:
1) That "in bed with the captain's daughter" was meant quite literally, but it was wholly a contrivance of later singers.
2) That "in bed with the captain's daughter" was an old lyric and that, being so, couldn't possibly (given historical context) be meant literally...and which case therefore it is a metaphor we've still determine.

Look at Masefield's version, above. Notice how it asks 'What shall we do?" about "drunken sailor", followed by an answer about what we shall do. THEN it moves on to ask about the drunken soldier, followed by an answer. The version that Doerflinger collected from Dick Maitland is the same. The version given by Harlow has exactly this style, but carries on the theme. He asks "What shall we do?" with:
drunken skipper
drunken chief mate
drunken steward, etc., each followed by an answer. This is as opposed to a long list of punishments for the "sailor." So, "What shall we do with the captain's daughter" fits that pattern...provided we get an answer! And it seems quite plausible that we *would* -- something rather bawdy, I'm sure. Writers may have avoided including the verse for that reason. (Hugill's statements suggest that one also might ask, "What shall we do with the Virgin Mary?"!)