Update Notification - Pulls Update from WP.org and not WPMUDev?

I installed this and had a notification got a notification to update 45 of the themes. I updated all of them without realising that the updates will be pulled from WP.org instead of WPMUDev. Now, I have to remove each one of the updated themes and put back the ones included in the Farm Pack.

I am new to this, question is, if there is an update from WPMUDev on any of the 133 themes, would that be notified in the WPMUDev update notification? So should I ignore the update notification from WP core?