In the Golden Dawn system, the path of Ghimel runs from Tiphareth to Kether. In Waite's Fellowship of the Rosy Cross, Daath is placed in the middle of this path creating two paths. As early as 1910 Waite is known to have been entertaining this idea. The following passages from his paper, "The Tarot and the Rosy Cross" are a couple of examples. Notice his description of Daath as the union of Binah and Chokmah. He also explains how the Portals aren't sephiroth but gates leading to them. He notes that the path of Ghimel goes directly to Kether bypassing Binah and Chokmah, but there should be a Portal in the path that connects to Binah and Chokmah, which in fact there is, Daath. He justifies the use of Daath as a Portal by noting that it isn't technically a sephira, but a sub-sephira. It's also a "centre of influence coming from Chokmah and Binah" so it's an ideal gate leading to them both. I've created a diagram that should make it easier to follow what he's saying.
"It should be observed in the meantime that in order to reach Tiphereth the Postulant re-enters Yesod, whence he proceeds upward to the threshold of the Second Order; and so it may be gathered—by the virtue of another inference—that the point of departure for the entrance into the Third Order will seem to be Tiphereth of necessity. But if the Postulant enters Atziluth by the help of a Portal it is not assuredly that of Kether, which would involve overstepping Binah and Chokmah, as if these were not stages of his progress; and the Portal of the Third Order must be therefore in the Path itself. In certain delineations of the Tree of Life there is the indication of a middle point in the Path of Ghimel, which point passes under the name of Daath, or Knowledge, and one reason—though of an exceedingly presumptive kind—why it may be the Portal of the Third Order is that Daath—like the Portal below—is not a Sephira, but the centre of influence coming from Chokmah and Binah. It is that which they produce between them, and there is a sense in which it stands for them both."—The Tarot and the Rosy Cross, c. 1910.
In another place in the same paper Waite explains further his point that the Portals aren't sephiroth, but "gates."
"Now, the Portal of the Golden Dawn is not a Sephira, but, as I have said, is the Court of Malkuth. The Portal of the Rosy Cross is not a Sephira, but the Gate of Tiphereth. And again, it is reasonable to infer that the Portal of the Third Order [Daath] is not a Sephira."
That Waite was thinking of this in his design of the High Priestess seem pretty self-evident to me. In his "Tarot and the Rosy Cross" paper he says it plainly. Speaking of Shekinah he says, "As the Shekinah in transcendence she manifests in the vestures of a High Priestess"; and, "She is the Guardian of the Gate of Daath." Check out the following diagram.
High Priestess Diagram
It will be seen that the orb on her crown falls exactly over Daath, and the horns point to Binah and Chokmah; the central orb represents the union of these two. The image on the right shows the High Priestess' path in Waite's FRC system. All the sephiroth are labeled except Malkuth which I don't believe is illustrated. Yesod is the crescent, the Moon being the planet corresponding to Yesod. Its yellow color is the same as the yellow in the pomegranates which seems to connect it with the other sephiroth.
There's something else which connects the High Priestess with Daath. For Waite, Daath was the central source for the rivers of Eden. In the GD, the rivers originated in the Supernal Eden—which was Kether, Chokmah and Binah combined into one—then divided in Daath:
"The River Naher flows forth from the Supernal Eden and in Daath it is divided into Four Heads."—Regardie, Complete Golden Dawn System of Magic.
Waite sees it differently:
"The Sephirotic Binah, or Understanding, has nothing to do with the river symbolism of the Sephirotic scheme, as this springs from the sub-Sephira which is called Daath, or Knowledge. . . ."—Waite's Introduction to Vaughan's Lumen de Lumine, 1910.
"The Rivers of Eden flow from a central source in Daath, which is the Higher Knowledge."—FRC Practicus Initiation.
This would explain the great body of water behind the High Priestess and the water flowing from the bottom of her robe.
Something else of interest is in the GD's symbol of the Supernal Eden. It was the "Woman clothed with the Sun and the Moon at her feet" as seen in this picture of "Eden Before the Fall" from Regardie's The Golden Dawn
Eden Before the Fall
The Sun is located approximately in the same place as the Solar Cross on the High Priestess, and the crescent at her feet.