PHP just has a different deployment model in most cases using just Apache + mod_php out of the box and PHP is embedded inside the Apache process.

This model is memory intensive and does not scale well.

A more accurate comparison would be something like Nginx + PHP+FPM or even HipHop VM for PHP.

If you're only measuring stick is "Upload your scripts and run, BAM!" then it's no real argument. But if you're at the scale of having professional systems engineers and scaling to millions of users then deployment isn't an issue as you have your processes running smoothly.

If you can deploy the same set up 10,000 times easily, it doesn't matter that the initial set up took you 2 hours vs. 1 hour.

Software is infinitely reproducible. The effective deployment cost then becomes 0.

Essentially, at scale, you are no longer running Apache + mod_php.