In P5, 16.1.2 gives nice examples of how to encode complicated footnotes assuming there is no footnote reference in the text (like a superscript number). You can either use "implicit pointing", putting the note element at the point of reference, or use "explicit" pointing, with a ptr element at the point of reference.
But what if there is a superscript number? Should you use ptr or ref? My inclination is to use ref, similar to the second TOC example in 4.5 (which has page number references, unlike the first TOC example). It seems to me that footnote references are such a common encoding need that P5 should be explicit about how to do this (with an example).