Use Sigil. Upload the validated epub to the KDP platform.
The one purpose I still use Word for is to build the endnotes. It does a splendid job, though a bit of tweaking does improve it.
Keep Calibre out of it.
Avoid Kindle Create. The only people I know who favor it also like playing about with software for the enjoyment they get from it. For lesser mortals, it's Pooh trap.
As a reader, I'm opposed to pop-up notes as distracting and unnecessary. If the note actually adds to the reading experience, then incorporate it into the text. If it's merely a citation, anybody interested in sources will be happy to click back and forth or, as I do, occasionally sit down and glance through the notes one after another.
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