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I converted your files to KFX and loaded them onto a Kindle Oasis via USB. They showed the same footnote behavior as seen in your images. The book "Converted file" book shows popup footnotes full screen.
I examined the EPUBs and resulting KFX files and could not find anything that would account for this difference.
I then tried those files in the Kindle Previewer and the Kindle for Android app. On both of those "Converted file" shows popup footnotes at the bottom of the screen, matching the behavior of "internet file".
My best guess is that the odd behavior is being caused by a bug in the KFX renderer on the e-ink Kindle platform.
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