One issue I was discussing with a colleague just the other day is that you cannot leave a comment on lines that are not "part of the diff" (changed or context), which is sometimes really useful for "see this thing over here".
(source: that’s one of the features that people like most about the review tool I created, CodeApprove)
I like to use that to surface cross-references (annotating anchors whose references appear in changed or context lines, and references whose anchors do).