Yes. Keep the ini_set code in your wp-config.php file. It is completely unrelated to any of these issues with Ownership or anything else with this issue.
I would phrase the question/request to your support folks like this so that you do not get a defensive response/reaction:
Currently on my WordPress website I am prompted with an authentication popup window since WordPress is using the ftpext Filesystem API Method. I would like to use this WordPress code: define('FS_METHOD', 'direct'); which will allow me to install things on my WordPress site and server without being prompted for authentication. I attempted to use this WordPress code, but when I attempt to install anything (a plugin, etc) the installation fails with this error message: Could not create directory. I assume this issue has to do with Ownership of folders/files or some other server configuration (suPHP, suEXEC) that does not allow the WordPress Filesystem API Method: “direct” to be used on my particular website/server. Would it be possible to change the server configuration so that I can use the WordPress Filesystem API Method: “direct” on my server?