1. Global php.ini – /opt/cpanel/ea-phpXX/root/etc/php.ini
2. The php-fpm pool files can contain php.ini values - for example, in cPanel, the php_admin_value pool conf[disable_functions] = x, y, z etc. that you can override by using the .yaml files and rebuilding the pool conf
3. The .user.ini file – It is important to note here that "Only INI parameters with PHP_INI_PERDIR and PHP_INI_USER modes will be recognized in INI files." – which means you can not put everything in it – The list of what can be put can be found at http://php.net/manual/en/ini.list.php. Look in the editable column and make sure that PHP_INI_PERDIR and PHP_INI_USER are present.