Right, but none of those are metaphorical punishments. They’re just literal things that seem funny. And it’s a folk song, so the variations and intended meanings are as ephemeral as a game of telephone. Having one line about sleeping with the captain’s daughter might have been even more amusing (and thus more catchy) because of the double meaning.
I’m not saying that it’s not possible that your interpretation is correct, but I would imagine that your average deck hand singing sea shanties isn’t thinking metaphorically when he’s singing about getting drunk and laid. And insisting that the one line in the song isn’t about fucking is feels like wishful thinking rather than a devotion to historical accuracy.