A quick search for "When I come back a loaf" gives only links to this thread, or to Captains Courageous, or to other sites which in turn link back to that book.

It looks suspiciously like the words were original to Kipling, and written for the book. While I've nothing to back that up, there does seem to be a lack of any contra-indications.

Also the construction of the verse:
Now Aprile is over and melted the snow,
And outer Noo Bedford we shortly must tow
suggests (to me) a verse being constructed on the spot. (possibly to fit with an established chorus)
If it was part of a longer song then other verses would probably relate to other sailings, and that (first?) verse would be "When April is over . . ."
Other verses could then start:
"When July is starting for Hartford we sail . . ." etc.


Cheers
Nigel