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As far as I know, once a reading system identifies a footnote as such, it displays it however that reading system prefers to show it. And a common way for a Kindle to identify em is via a backlink, which both of your examples seem to include. I would be curious to know whether the behavior differed between those two examples. I didn’t think that changed based on whether they were shoved over to a separate file, though it’s generally considered better that they not be.
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