[Quoth]

You can't or shouldn't exactly duplicate how a paper book works as an ebook. It does links back and forth well. But you absolutely can't mimic the paper style of a source for a footnote. People need a larger area to tap on.

The ONLY sensible way to do it is how I suggest. I know it's more work, but it's far better quality, more reliable and safer to manually number.

Word (and InDesign) are designed for paper. Both predate ebooks (InDesign is ancient and kludged and may have bits of Pagemaker in it). Though ebooks are based on HTML and CSS, they certainly don't work the same way as web pages or web sites.

I've been creating content on computers since 1979 and used to teach this stuff. Do things to suit epub and get a Sage 8″ Kobo to proof on and copy back annotations to Calibre, then copy/paste to a text editor window beside Word or LO Writer.
It's then trivial to edit styles and page formats of a copy of Word/LO file to suit paper/POD/PDF. Working the other way (editing & styling for paper and trying to get an epub to work) is very very much harder.

It makes no difference that you are editing OCR from an old paper edition rather than writing from scratch. It just means the creative bit is replaced by proof comparison with the paper.