I don’t know if, as an XWiki user and not developer, I’m allowed to open threads in this section, but I was commenting the Jira issue in the title when I had a doubt about whether what I was going to write would correctly fit there or should be discussed on the forum beforehand.
So here’s the other half of my comment entered at: Loading...
I found that issue while searching about the footnotes macro and gladly found that the behaviour I noticed had already been reported. Given what’s in that issue, I’d like to suggest the following.
I’ll only refer to PDF exports here, but that’s because I do not know all the XWiki export options, so there’s surely things I’m missing here.
What is currently implemented by the Footnote macro (and its compation Putfootnotes) is really endnotes: they’re rendered at the bottom of the XWiki web page and in the last page of a PDF export that results in several pages out of a single XWiki page (see How to Use Footnotes and Endnotes | Proofed's Writing Tips).
So, a new macro should be added, i.e. Put Endnote; it’s behavout should be the same as the current Footnote macro: a marker is added near the word where the note is entered and it’s content is shown (or printed) at the botton of the webpage (at the bottom of the last page in a PDF export).
This will automatically resolve almost all issues about footnotes misplacements etc. since nobody should expect to have a note at the end of the printed page if he entered an endnote - saying “almost” because I think notes could use little improvements - but that’s another thread (cough Footnotes putfootnotes print or PDF export cough 
).
And given that XWiki is not a layout / typesetting software, this could be enough: the Footnotes macro can be retired and footnotes are simply not supported.
Of course, supporting footnotes would be nice, but now their implementation can be more easily addressed, they can be marked wip / experimental etc. even depending on what Paged.js supports.