You need to get footnote handling more similar for eBook and PDF output. I had to let Scrivener nail its “horizontal line” and footnotes at the end of my last page, which happened to be “about the Author”. I should really be able to create an Endnotes document “near” the end of the book and force Scrivener to use it. Of course, there had better not be any footnotes after that page…
You can use the <$–ENDNOTES–> placeholder tag to tell Scrivener where in the text to place endnotes - see “Placeholder Tags List…” under the Help menu.