They run their PHP on HHVM for one:
https://en.m.wikipedia.org/wiki/HipHop_for_PHP
https://github.com/facebook/hhvm
...and yeah, it executes PHP code, for sure. But right there, things are already different, and the reality is that they've written a substantial code base in C/C++.
And, two, I'm sure they retain some serious business proprietary trade secrets about their server infrastructure, meaning that while the web front-end might render out HTML like a souped-up CDN, behind the scenes, there is a shit ton of other stuff going down.
Honestly, I think they just leave the file name extensions in the URL for the sake of nostalgia.
Also their frontend is the only thing written in PHP. You hit the site, you're hitting PHP pages.. Not just an extension for nostalgic reasons.