Hi
This is another problem people using LibreOffice and Writer2xhtml do not have to worry with.
They select either Style/superscript or Insert/endnote while textprocessing to write (nothing really unusual) and when they export to EPUB, this is how the end result looks like: (This is a Sigil view extract, text on top, code lower)
Of course, if you are not happy with the style you can modify character styles or endnotes characteristics in LibO like you wish to suit your needs.