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I have hoped to do the same as you have proposed, that is, to have the note pop up in a new small window on the page, which you can do in a web page, of course. But I think it is not yet possible in a straight epub system, only if you format your book as an ibook app or similar. What I settled on which does work is to make my text links to a note in a separate section of end notes and then link the end note back to the point in the text that you just left. This works smoothly in epubs, mobi, and in Sigil. The linking in your document can be done at any stage in the process.
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