It appears that the path.prefix is only honored in the twig templates and not in the redirects from the backend. For example, the deleteSubmit() controller action redirects using the following, which simply redirects to the domain root, /.
$this->app->redirect($this->app->urlFor('home'));
If i'm hosting xhgui at https://mydomain.com/tools/xhgui/ and i have path.prefix set to /tools/xhgui/, after a delete i will be redirected to https://mydomain.com
Not a huge bug by any means but a minor annoyance.