In Kloxo-MR 'rule', every files (except in defaults, domains and webmails), Kloxo-MR will choose their 'custom' file instead their 'original' files. So, Kloxo-MR will read/process (with running 'sh /script/fixweb' in webserver context) custom.php-fpm.conf instead php-fpm.conf. What's is 'custom' files?. This file is copy of 'original' files and we can modified it.
Every 'original' files possible overwrite Kloxo-MR in KLoxo-MR update process.