Reposting my comment from the blog:

Browsers are the one responsible for providing the referer information to the web server. If you come from somewhere that isn't a browser page, it is sent without a referer (and considered a "direct link")

I wish I could track visits from external apps and bookmarks, but there are some privacy concerns, too.

This is because they'll be being launched as a plain URL by the desktop app. It just says "Operating System, please open this URL."

Is there even a standard/cross-browser method of saying "Please open this URL, and here is a referrer to use."?