I have WebMin version 1.65 install. When I go to Backup Configuration, an option for PHP is not listed, even though I have the PHP module installed. I examine the backup file directly and the only PHP related file is etc/httpd/conf.d/php.conf. See screenshot:
It should backup /etc/php.ini, /etc/php.d/
Thanks for pointing this out - this will be fixed in the next Webmin release.