My next suggestion was to go to the KOReader subforum, install KOReader:
https://www.mobileread.com/forums/sh...d.php?t=314220
(see the 2nd post in that thread), and see if the footnotes look better there. I don't use KOReader (I don't appear smart enough to figure it out), but I tried it and I can't even get footnotes to open (too persnickety). But, you could try it and see how your experience is.