Great plugin — simple and minimal design, love it.
However, quite a lot of themes don't rely on the
the_author_uri functions, but use more specific queries. The widely used Hybrid (and all its spinoffs and child themes) for instance uses
get_author_posts_url(get_the_author_meta('ID') to construct its entry-author shortcode. As a consequence, Custom Author Byline doesn't work out of the box with most Hybrid-based themes.
The best way to make Custom Author Byline compatible with an as wide range of themes as possible is probably to filter all author-related function calls and not just the two most general wrappers. I would love to hear from the plugin author about the plans for future development for wider compatibility.