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Perhaps instead of using header tags in your footnotes, you could use appropriately styled p tags?
And yes, Sigil's ToC build code builds the ToC based on the use of h1-h6 tags. That's the purpose of h tags given the common definition I've seen in multiple places is "the <h1> to <h6> tags are used to define HTML headings".
Personally, I use h1 tags for books in a multi-book omnibus, h2 for parts within a book, h3 for chapters & h4 for sections within a chapter. The only time I used h5 & h6 was in one textbook which was a (IMNSHO) dog's breakfast considering over 1,300 entries in the xhtml ToC file made it almost useless on most devices/apps that didn't support ToC collapsing.
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