InDesign is primarily for paper.
Create a good styled docx and import to Calibre and convert to epub is better (and if you use odt files on LO Writer with an extra Save As in docx, it's free).
Fixed Layout is like an epub version of PDF, so since InDesign is good for PDF that works. But Fixedlayout doesn't work on many apps, or readers or small screens. PDF is preferable to Fixed Layout epub, but neither makes good ebooks (which must reflow to suit screen).
Footnotes are tricky and there are 3 methods. The snag is there is no "page bottom" in real ebooks. So each footnote needs to be a separate paragraph after a chapter and linked (entire word and [3] etc number so it can easily be tapped. Then the footnote needs to have a link called [back] to the original location. Popup footnotes are unreliable and only some devices/apps.
If it's a short comment of a few words then putting it right justified just after the paragraph works well on ereaders. Some don't have touch screens (even new ones) and then you have to use navigation buttons to the link.
[A short note]
Then the next paragraph.
It's a mistake to too closely replicate paper books unless it's a PDF. Fixed Layout epub is a book-replica format as an alternative to PDF with slightly more user-side flexibility. Really for 10″ or larger screens.