Both PHP and Apache got rebuilt to make the package more robust and usable for most people. As for Apache, the doinst.sh script now forces to install the new rc.httpd in /etc/rc.d so that people will always have the latest changes. I think it's needed due to changes of the pid location from /var/run/httpd/ to /var/run.
As for PHP rebuilt, it's because there's a difference with how the autoconfigure works in 32 and 64 bit architecture. In 64 bit architecture, there was no problem with thread safe as it's handled automatically by the autoconfigure, but it's not the case in 32 bit system. So the solution is to give an explicit parameter --enable-maintainer-zts so that it compiles fine on 32 bit as well.