Thats no bug. It is intended that the line is commented out as this kind of configuration does not work for mod_php when you have more then one vhost on a server that has this configuration line in the vhost file. If this line is active in a second vhost, then apache will not start anymore. The reason for that is simple, php can load only one configuration per process, as all websites with mod_php share the same process, there can only be one php.ini for all mod_php websites.
The custom php.ini settings are only for php-cgi, php-fcgi and suphp as explained in the manual, chapter 22.214.171.124. For mod_php, use the php_admin_flag and php_value options of the mod_php module in the apache directives field.