[kovidgoyal]

Reference mode only works with <p> tags, it doesn't care about classes. This is because <div> tags can be nested, so there is no good way of getting a single useful number out of them, the same visual position in the book could correspond to several different nested <div>s. And you would get weird jumps in numbering, for example, if the visually first para is numbered 1, the visually second one may or may not be numbered 2 depedning on the presence of nested divs.