FWIW, if you're on the web UI, you can leave a private note to the author by highlighting some of the body text, then picking the note icon from the pop-up. Makes it easier for the author to figure out where exactly a word or phrase you're commenting about is as it's tied to that text you highlighted.

Medium lets authors turn private notes off, but I don't see a good reason for them to do so - and most do not.