Go to '/opt/<phpXYm>/etc/php.d' and you can see some .nonini files (like ioncube). Example, copy opcache.nonini to opcache_used.ini.
You can update phpXYm with 'sh /script/phpm-updater php54m' or 'sh /script/phpm-all-install'.
Custom php.ini not possible at this moment and no needed.