It’s working for me (using the same version of Caddy). The problem is with your browser.
Firefox 54.0 is sending Accept-Encoding: gzip, deflate. Caddy can’t serve the Brotli file in this case because Firefox didn’t ask for it.
On the other hand, Chrome 58.0.3029.110 sends Accept-Encoding: gzip, deflate, sdch, br. Since Chrome indicated that it would accept Brotli-encoded files, Caddy will serve me a Brotli-encoded file.
By the way, I have the same problem when the file is gzipped (i.e. I have a single file in my folder: index.html.gz that is a valid Gzipped HTML file).