Why should you do ./build secure_php every time?
You just need to do this once, then a secure php.ini is created.
Then you edit the /usr/local/lib/php.ini file, change your disable_functions in whatever you want it, save the file and restart apache and you're done.
If you need any changes later on, you change that file again and restart apache. There is no need to do a ./build secure_php multiple times.
In the /usr/local/directadmin/custombuild/options.conf file, maybe you have:
You can set those to "no", since you already have a good php.ini so a secure php.
I don't work with the plugin so I only know how to change this via console.
Either edit the file, save it and do a ./build update or:
./build set php_ini no
./build set secure_php no