You are correct we are not to add line numbers.
The notes are placed in the order in which they occur on the page. Do you think this might be more appropriately treated as marginal labels? Especially if there isn't a specific point within a paragraph that it applies to?
If every paragraph is marked, it might be easier for the reader if you DID include the line numbers. I guess I don't really know enough about your print. But if every paragraph is marked, the marginal label guidelines really wouldn't work well either.