I cannot see any way to highlight or take a note on a footnote in a resource. Many books have extensive content footnotes that have important information (even if not central to the main argument in the book). The ability to highlight and comment on these footnotes is critical for serious study of a scholarly monograph or reference book.
My work around is to copy and paste the quotation and then make a note on the footnote. But this wastes a lot of time compared to highlighting while you read.