I really like this question, too. Thanks for asking and sharing your thoughts! I am going to reblog my response on Blessing All the Birds, too, even though this is not directly related to feminism.
The line you are reference here has always been a piece of Joanna’s poetry I felt I immediately understood: it is a beautiful and touching way to express loss, personal disorder, and a seeming inability to cope with change (“…but I have never known the way to border them in…”).
If I were to take a stab at what I believe “Emily” as a song could be chronicling, I would say that at its most basic level, the narrator (Joanna) tries to find healing from catastrophe, from isolation, from dislocation, and from rumor by going back home and reaffirming her familial relationships with primarily her sister and then her father towards the end of the narrative. Home, family, and healing in this song are all intimately tied to nature and to memory. The chorus is an expression of a memory bound in nature, a moment of bonding between two sisters, one an artist and one a scientist, as they sit by a river and look up at the heavens.
The narrator’s goal in “Emily” seems to be to find rebirth. Emily, the character, helps Joanna achieve this rebirth primarily through a (re)communion with nature, a nature which is both terrestrial and celestial. The narrator colors the rebirth theme throughout the song with very Christian symbols and concerns by casting Emily as a Jesus figure (for more on the role of Christianity and its iconography in “Emily” and the whole of Ys, see this post from bonefromthevoid, who very much influenced parts of my analysis in this essay and who really just gets Ys at a deep and impressive level). The whole concept of rebirth has had deeply Christian connotations for millennia and rebirth for even longer than that has been tied to cleansing with water (and that is precisely why Christianity incorporated it into its mythology and religious practices from pagan religions). The rebirth imagery throughout the song is also emphasized by mentions of midwives and motherlessness. Emily is not only Jesus, she is a mother, both images of self-sacrifice and protection.
After the (re)communion with nature (and thus, family and memory) is complete, Joanna revels in the “sweetness of being,” but this sweetness is juxtaposed and undermined throughout that verse with imagery and reminders of hers and our own mortality. The Christian sacrament of communion which Joanna explicitly references in this verse (“take this and eat this”) commemorates that very paradox of life and death: the Eucharist promises those who eat it a blessed existence on earth and a blessed existence in heaven. But the Eucharist is the physical embodiment of Christ’s mortal corpse. As they eat the Eucharist, they are eating life and death. And we must consider that rebirth itself is a form of death. What happens to the self which came before?
The narrator seeks rebirth throughout Ys, a complicated matter that I do not at all claim to comprehend very meaningfully. I probably only understand about one percent of Joanna Newsom’s corpus at a very deep level since all of her songs are teeming with different symbolic, thematic, and narratological resonances which are still quite mysterious to me, even as a very dedicated consumer of her music and poetry. And that is why I feel most comfortable analyzing her corpus from a feminist lens, an analytical framework in which I can claim some expertise. But anyway…I can confidantly say that Joanna on Ys heavily connects rebirth to water and to death (see “Monkey & Bear”) and to nature generally (see the end of “Only Skin” where her bones are buried).
Lastly, just to address your cool connection between “Emily” and “Soft as Chalk,” Joanna describes the narrator’s “sanatorium” as a place rooted in nature and responding to nature, a description which really comes as no surprise considering the connections between healing and nature all over “Emily” and Ys. “Soft as Chalk” even has all that dove imagery, drawing it even closer to Emily symbolically. If we consider the narrator the same on Ys and Have One on Me (which I think is a fair thing to assume), finding comfort in times of hardship in the physical world is an important part of her characterization.