We are rolling our own software version for NGiNX, Apache2, and PHP but we do not change any source code of any software that we have mentioned above.
Rolling our own software with different configuration from Ubuntu standard repository is crucial to allow us to tweak and modify each software config easier. For example, the standard Ubuntu repository will prevent you from installing PHP5.5 alongside PHP5.6. The only way to achieve this is to compile your own PHP and that is what we are doing. So you can use multiple PHP version inside your server(s) depending on your web application needs.