I believe the confusion arises because Pentangle chose to fit "Twa Sisters" (Child #10) verses to the "Riddles Wisely Expounded" (Child #1) tune and chorus. Bronson offers no "lay the bent to the bonny broom" refrain in his definitive collection of Child #10 versions, while it is the very first version he reports of Child #1 (from D'Urfey).

I remembered reading an explanation of the phrase somewhere, and finally found a reference to it in Wimberley's Folklore in the English and Scottish Ballads (1928), pp 350/351. I'll quote it extensively, so please forgive my usual typos. Referring to Lucy Broadwood's (1908), Wimberley wrote:

Miss Broadwood's observations on the magical properties of plants represented in the burdens of The Elfin Knight (2) and Riddles Wisely Expounded (1) may be summarized as follows: parsley, used by the ancient Greeks at funerals, and on graves, and employed magically in Germany, the British Isles, and in Europe generally; sage, a magic plant in England, and proof against the evil eye in Spain, Portugal, etc.; rosemary, called "Alicrum" or "Elfin Plant" in Spain and Portugal, is worn there against the evil eye, burnt against witches in Devonshire, and everywhere else associated with funerals and death; thyme, a chief ingredient in a recipe (ca. 1600) for an eye-salve for beholding without danger the most potent fairy or spirit, and associated with death and the grave in England; juniper, sacred to the Virgin in Italy and France, and especially potent against evil spirits; the gentle (thorn or bush), the name used all over Ireland for the large hawthorns which are regarded as holy and sacred to the "gentry" -- "gentle people" or fairies who inhabit them; holly and ivy, used magically from the earliest heathen times, holly being particularly abhorred by witches in England and other countries of Europe; broom, most potent against witches and spirits, and per contra, often used by witches in their spells; the bent or rush, protective against the evil eye, and, as Miss Broadwood points out, doubly powerful when combined with the broom, as in the refrain (1 A), "Lay the bent to the bonny broom." We may dismiss the subject of the incantation refrain by quoting a note from Scott, which goes no little way toward proving Miss Broadwood's point that our plant burdens are incantations directed against evil spirits:

The herb vervain, revered by the Druids, was also reckoned a powerful charm by the common people; and the author recollects a popular rhyme, supposed to be addressed to a young woman by the devil, who attempted to seduce her in the shape of a handsome young man:--

"Gin ye wish to be leman mine,
Lay off the St. John's wort and the vervine."

By his repugnance to these sacred plants, his mistress discovered the cloven foot.

Okay, after all that, I should point out that "Riddles Wisely Expounded" is a riddling contest between a woman and an evil spirit, usually assumed to be the Devil himself, or "Old Clootie," as he is known without actually naming him, a safer practice. Therefore, the combination of the bent and broom as a means of warding off the Devil is appropriate in the ballad to which the refrain is properly attached. It has nothing to do with the story of the "Twa Sisters," I fear, accept that Pentangle like the melody to the one and applied it to the other. Of course, in many versions of the "Twa Sisters" the bones and hair of the victim manage to magically accuse the murderess through the music of harp or fiddle, but while this is mysterious, it is not Satanic.

And, finally, I also read somewhere else, and can't for the life of me remember where right now, that Miss Broadwood's theory was pure folkloric fantasy. I don't care; I like it!

Hope all this helps a bit.

Sandy