A tree structure of ideas naturally fits into a linear essay of text, so I don't understand this. The opening paragraphs of a section of text are a broad theme on which subsequent paragraphs expand. Paragraphs also carry a similar structure in their sentences, and every great essay builds large trees of logical ideas within a linear rhetorical structure. A footnote as an expansion is a crutch: either the text of the footnote is important enough to appear on the page, in which case you should generally find a way to put it in the prose, or it is not, in which case you should omit it entirely.

The only truly good use of expository footnotes is to expand on things that the reader might be interested in (and point to further reading), but are orthogonal to the main argument of the essay. They are not for expansion of the tree of logical arguments present in the body of the essay.