It's not only PHP that chunks the data; it's actually the job of Apache (or Tomcat etc) to do this. That's why the default is to turn off the "chunking" in PHP and leave it to Apache. Even if you force a flush from PHP, it still can get trapped by Apache. From the manual:
flush() may not be able to override the buffering scheme of your web
server and it has no effect on any client-side buffering in the
browser. It also doesn't affect PHP's userspace output buffering
mechanism. This means you will have to call both ob_flush() and
flush() to flush the ob output buffers if you are using those.
There's a Wikipedia article on transfer encoding / chunking: http://en.wikipedia.org/wiki/Chunked_transfer_encoding
Apache gets more complicated with GZIP or deflate encoding; you'll need to hit an apache server as to how you chan configure it.