I have two V3 PFD-style books in progress. One has all of the footnotes at the end and the other has them at the bottom of pages. I have the Compile => Foot & Endnote settings the same. I have an Endnote page just before the back matter with the magic endnote placeholder.
Have you tried to change this here (and make sure you are turning footnotes into endnotes):
I just tested on a test project and switching between End of Document and Before page breaks is working for a PDF compile here, though I didn’t have a special <$–ENDNOTES–> document…
That was the first thing that I set, but I they still show up at the bottom of pages. After AL LOT more searching I found two more settings that are required on the Compile General settings
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No doubt one of them is the other compile setting mentioned by nontroppo: “and make sure you are turning footnotes into endnotes” – which is under the gear icon in the right panel of the main Compile dialog.