<li ="notes">
This is missing the complete element equation 'class=' in several spots. Is this causing the problem?
https://epubknowledge.com/docs/notes
Backtracking a bit...at this web link above they use an attribute <a epub:type="pagebreak"...> after the last note, just the very way you were hoping to avoid doing it.
As a side thought...pagebreak as zero height?
.pagebreak-height {
min-height: 0;
max-height: 0;
height: 0;
)