I've seen some apps that change the highlight style, or add a small icon somewhere like at the beginning of the highlight. A few apps use a post-it note like icon in the margin. For a heavily marked up book, being able to find specifically notes, which are of more significance than highlights, I think that is most easy to see. Imagine quickly flipping through pages to find an annotations, seeing an icon in the margin is quickest. Do I believe the horizontal margins on iPhone should be made slightly smaller to accommodate that? Yes. See iBooks and Google Books for examples. Maybe there's another way that is more visually distinct and easier to find, but I can't think of one.
I've seen some apps that change the highlight style, or add a small icon somewhere like at the beginning of the highlight. A few apps use a post-it note like icon in the margin. For a heavily marked up book, being able to find specifically notes, which are of more significance than highlights, I think that is most easy to see. Imagine quickly flipping through pages to find an annotations, seeing an icon in the margin is quickest. Do I believe the horizontal margins on iPhone should be made slightly smaller to accommodate that? Yes. See iBooks and Google Books for examples. Maybe there's another way that is more visually distinct and easier to find, but I can't think of one.