I think he's referencing the fact that turning that off will allow the necessary includes but will also allow instances of "Joomla" to still appear in your site allow bots and potentials hackers to fingerprint your site.
1. In some people's installations, they do not have includes being used bearing the word "joomla" so they can have the word "Joomla" edited out.
2. In other cases, such as yours, there are files being included with the word "joomla" in the path that don't get included correctly because that info is being edited out. Our plugin COULD be modified so that it finds the files and renames them, though editing the Joomla core is typically a bad idea.
I'll look into adding an option to choose whether lowercase "joomla" gets edited out which would allow "Joomla!" and "Joomla" to be removed but not little "joomla" that we would need for our file includes. This would prevent your site from saying Joomla in search engines but, of course, would not make your site as incognito as to the CMS it's running.
It may be more practical to rename that file and edit the code that includes it.
What are your thoughts?
Kindest regards,