OK, I hope that’s an easy fix.
In a book, go top menu - second tab - Style Tweaks. Now, find the one that says something like “show footnotes in the page” (that makes it work after all) that target regular p.footnote.
Now you need to make another css rule that has the same content but targets this new p.foot-ind. You can test this quickly by copying the whole output of the window from original style tweak, then going to second tab - style tweaks - book specific tweaks. Hit apply.
After this you add a permanent fix in styletweaks folder with a new css file, which (after a restart of KOReader) you will be able to toggle in other books.
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