I haven't run into this for any of the fics I've podficced but a great example to listen to would be the pro audiobook for Good Omens. I listened to that story before I ever saw the print of it and never really realized that there were footnotes in the text, the reader did such a good job of incorporating it into the reading (that's not to say he changed the text, he just included the footnotes as an aside to what he was reading that felt totally natural in a conversational way).