I'm not a professional epub creator. Just a guy who has created a few books for my own use. Some family histories and cook books and such. When copying a family history that someone else wrote I don't feel it's my job to re-write paragraphs to include footnotes that others have created. I just look for a way to make reading easier for my family. The approach of boxing a foot note directly after the reference paragraph works for them.
I know that the pros have definite opinions about this and as an old publisher I can respect that. But as an amatuer now, I just want a simple solution that works for my very limited audience. Modern technology that allows me to do this is amazing. Sigil is an awesome tool for both us amateurs and you pros.