Endnote are - to the best of my knowledge - not supported by Google Docs. I think the simplest way to add an endnote is to do it manually: insert a number in the text, change it to a superscript number, then write the corresponding number and note manually at the end of the document.
Your workaround may work just as well, but since adding such notes to documents is not a function of Paperpile I would not recommend it; it would add unnecessary clutter to your library.