Actually, Roud 1354 maps to two essentially different songs. Both are titled "William of the Waggon Train" in broadsides and feature the ubiquitous William and Nancy in the general situation of Nancy going to war with her lover. But they're different in meter and have no overlap in text or events. The apparently earlier one typically begins "Attend awhile, and do not smile young men and maids around", and jumps right into the pair going off to war, where they're both wounded and die, though not before Nancy can dash off a letter to a friend and seal it with her gore--nice touch. Most broadsides give the tune as "Bushes and Briers", but metrically this ballad doesn't fit the "Sister and the Serpent" pattern, so it's doubtful "Bushes and Briers" would be the "Waggon Train" tune of Paul's reference. For what it's worth, Sabine Baring-Gould collected another tune for this song (SBG/1/3/425), noting that it's a variant of "The Country Farmer's Son".

The other text typically begins "One lovely morning as I was walking, In the merry month of May," and deals only with their preparing to go to war together. It has the same metrical pattern as "The Sister and the Serpent". Here, most of the tunes collected are variants of "Rosetta and Her Gay Ploughboy", which (despite its jauntiness) was also used for the murder ballad "Eli Sykes". I posit that this is the actual tune meant.

The Baker/Collinson tune belongs to the "One lovely morning" text family, but is not of the Rosetta tune family. I hear a strong resemblance in the second half to Peter Bellamy's setting for "Andrew Rose & the Cruel Ship's Captain" in his Maritime England Suite. Any idea whether that was a traditional "Andrew Rose" tune, a borrowed tune from another song or a Bellamy original? It may furnish a clue as to the Baker tune origin.