Kindle creating endnotes and pop up footnotes - export to epub

And, sorry, I may have misread the focus of your question.

Footnotes have to go somewhere in an EPUB/Kindle file. If you select End of Section or Pop-Up, they exist at the end of the document; the only difference is whether the reader teleports you to them via a link, or makes them magically appear in a pop-up. That's entirely reader-driven behavior and it varies between readers.

In Kindle, the footnotes will be the last text element in the document, followed by the separate text frame for the end notes (if any  — and now I see you don't have endnotes, but were referring to the block of footnotes as end notes).

And the behavior is the same in EPUB, at least in Calibre and Thorium. If Apple has some magic trick to hide the footnotes as a block, that's nice... but it's one more variation from the standard that makes creating commercial EPUBs a pain the ASCII.

So you can have pop-ups or links, but the footnotes will be there at the end of your document in "conforming" EPUB and Kindle.

(Me, I use after-paragraph footnotes and format them to be unobtrusive in the running text flow, but that may not work well for poetry.)

Just to be clear, EPUB and the various Kindle formats are not the same thing. It is relatively easy to export to EPUB from InDesign, especially to an EPUB seller/portal like Apple, although Apple's implementation of EPUB is nonstandard and you have to correct for some quirks. If you have any intention of releasing to more general EPUB portals, you will probably need to fine-tune that version using a vanilla, standards-based reader such as Calibre. (Hardly any two EPUB readers render a file the same way; you have to pick your specific reader or optimize for the most standard ones and let everyone else take their chance.)

Kindle is a complete format conversion and can be much more temperamental about details, especially end notes, and especially-especially endnotes when used in conjunction with footnotes. Compounding the problem is that if the text is imported from Word, there are many more points of.... call it breakage, where things go poorly. You should expect a slow road getting to the first fully satisfactory book.

Also, poetry — I'll say this because it's common, but don't use soft returns to format stanzas. If you need five paragraph styles to accommodate various indents and so forth, so be it. EPUB does not handle soft returns well.

Happy to answer questions as you need answers. 🙂