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Actually I have read documents that had the footnote in a paragraph just after its reference. This actually was pretty easy to read I felt but is not standard as compared to a paper book. The current format seems ok to me but if you want to make it like a paper book then that's a different matter.
There is currently no defined standard for eBooks. Note that the way epub is headed is to place the footnote inside a title line that is placed in the enclosing tag as an attribute. In html today you can hover over a piece of text and the footnote would appear. At some point a similar idea would be you could click the footnote reference and a block would open up over the top of the page with the footnote data. Today no eBook reader supports this that I know of.
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