You could try to edit the options.conf file and edit the PHP version. Then rebuild the environment, but mind the fact dat PHP 5.3 is not out-of-the-box compatible with MySQLi.
what do you mean about the configure.php rewrited by the build ?
because i have this problem..
i put some line in /usr/local/directadmin/custombuild/custom/suphp/configure.php6 and when i start the ./build php n .. its change line in configure.php6