The implication is that writing code that uses PHP's built-in libraries is pretty fast, but the more you write in PHP itself, the slower it gets. For example, my impression is that Yahoo isnt really written in PHP - its written in C patched together using PHP.
The Zend engine was "rewritten" for PHP 4, PHP 5, and to a certain extent for PHP 5.1. I guess it wasn't a complete rewrite because the legacy code from about 10 years ago is still in there. Anyway, its still dirty, badly written, slow, and very very badly commented. Hacks abound (and not the good kind).