I see from your kepub hyphenation patch, you have a way to modify the kepub style sheet.
I also see from another
post that chopped off bits of characters can be made to display correctly if a small amount of padding is added.
Adding the two bits of information and knowing nothing about the whole thing, I wondered if it's possible to create a patch to add a small amount of padding to the top of the kepub style sheet and if this would prevent the tops of tall characters being chopped off and displayed at the bottom of the previous page.