Does single site admin see other plugins under “Plugins” menu at your configuration?
There should be the way to tell WPEngine that your update to wp-config.php is legal and should not be stripped. Other way it loses the sense as you can not customize WP configuration for your own needs.
You are right about ‘Enable “unfiltered_html” capability” option. So I will just hide the other options from local admin, not the whole “Multisite” tab. Thanks.