There is a huge difference between raw PHP and CakePHP. I'd be curious to see other PHP frameworks (such as Zend, or Slim) in there-- is Cake just particularly slow, or is that simply what happens when you have a PHP framework?
And if this is the case with their configuration of PHP, it makes me wonder what other platforms are not configured for production in this benchmark :)
It's no accident that zend optimizer (bytecode cache) is being bundled into php 5.5 as open source, as mere bytecode caching is now not fast enough to charge money for when hhvm is open source. I expect the next version of zend's commercial php server product to contain a JIT engine to match what hhvm can do.
I really hope the author picks up on this and compares it. It could provide some tremendous insights into pushing PHP further into this space.