BPS Pro has this Pro-Tool: WP Automatic Update which allows you to choose and set WP automatic update preference settings for each of your websites. By default WordPress automatically installs minor WP updates. It is up to you to decide if you want to allow major WP Automatic Updates. Personally I would only allow minor updates and then when a WP major version release is available I would do the installation from each website itself instead of doing that remotely from a 3rd party application like MainWP. I am old school Microsoft trained so even doing a remote installation at all from a 3rd party site is taboo by Microsoft standards. 😉