When you re-compile apache and php do you have to re-set all php configs. again ?
(disable_functions and open_basedir and etc)

Not generally. You have to watch for what the rebuild script is doing for you.

On the systems that I manage, it doesn't touch the httpd.conf file, or the php.ini file, so I don't worry about it :)

My httpd.conf is still normal with no change there was a reset on the php settings from 4.3.8 upgrading to 4.3.9.

Never mind I already used a backup php config.