[Quoth]

Don't use Word (or LO ) footnote numbering, or indeed "Insert footnote/endnote" feature at all, it has to be manually done. Explicitly number and link the word and number as one link to an explicitly numbered separate paragraph with anchor/bookmark. Put an anchor/book mark also at source and the word [back] with a link.

Why?
Delete a source number and the associated note can vanish in Word.

Never auto number lists or footnotes. Explicitly add them for 100% reliable.

have a psuedo chapter of notes, one per paragraph after the chapter so that this is separate file in the epub.

Only one-to-one footnotes. Repeat it if used more than once, because every note needs a text link [back], because many apps and ereaders have no "back" button, or the footnote may not be a popup.

Ebooks use html and css but are not websites.
Automatic footnote / endnote generation is buggy in Word and LO Writer, especially feature where if you delete reference in source paragraph the note can vanish.

Only use a numbered superscript on files for paper. For ebook use regular size and make preceeding word also part of the link. People have fat fingers compared to [2] to tap on.

Don't use Insert footnote/endnote (automatic process) at all, in any wordprocessor. Type a paragraph for each note and link manually, to and back.

For lists, create a paragraph style that mimics a list and type the numbers explicitly. Also beware fonts needed for bulleted lists. Automatic list support and especially numbering is erraticly or not at all supported in ebooks.