Pimcore\Config::setFlag PHP Method

    public static function setFlag($name, $value)
    {
        $settings = self::getSystemConfig()->toArray();
        if (!isset($settings["flags"])) {
            $settings["flags"] = [];
        }
        $settings["flags"][$name] = $value;
        $configFile = \Pimcore\Config::locateConfigFile("system.php");
        File::putPhpFile($configFile, to_php_data_file_format($settings));
    }

<?php

\Pimcore\Config::setFlag("useZendDate", true);