I am trying to solve this:

I got couple of domains I want to run under one PHP script. I wonder if there is an apache/php mod that would allow me to edit DNS records directly on the server. However, I need to assign the domains from within the script

It is a dedicated server, so installing additional packages is not an issue.

Any ideas?

In that case and if you are using BIND, try the mysql db driver. http://mysql-bind.sourceforge.net/
Documentation and install instruction (Warning, you need to recompile BIND to take advantage of this): http://mysql-bind.sourceforge.net/docs.php
It allows you to store BIND dns zone configurations in a mysql db rather that in a file.
It would be the easiest way.