The reason this happens is when the templates from their selected style are stored in the Database instead of using the Filesystem.
Another case for just dumping the internal style editors which store information in the database?
if (isset($user->theme['template_storedb']) && $user->theme['template_storedb'])if ($this->root == $phpbb_root_path . 'styles/' . $user->theme['template_path'] . '/template' && isset($user->theme['template_storedb']) && $user->theme['template_storedb'])