In case anybody's interested: the answer to my original question (how to replace php_admin_value by php_value) is /usr/local/ispconfig/server/conf/vhost.conf.master (on CentOS 6, perhaps might be located elsewhere on different distros). This file seems to be a template used by ISPconfig when constructing Apache conf file for each website. I have modified it and it seems to work and to have no unwanted side-effect. This seems to me to be "cleaner" approach than having both php_admin_value and php_value for the same config var in the conf file.
I hope this information might help somebody. In case I'm wrong about it, please someone correct me.
Last edited by ispconfig_question; 24th January 2012 at 23:22.