I now compose a lot in an old iteration of Word, using Mike Petrie's WordStar add-in to speed things along. I've found that Word's footnoting is brilliant. It needs a bit of editing before it looks right to me, but the go-to and go-back urls save a lot of effort on my part.
I do however move the go-back anchor back to the beginning of the sentence or paragraph, so the reader returns to a more logical spot rather than the actual footnoted word.
These are back-of-the book notes, not pop-ups.
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