Can I mute routine Configuration Protection notifications?

Yes. Open Settings > Application > Notifications and Dock and turn off Receive configuration protection notifications. The option appears when App notification style is set to Notification Center.

Configuration Protection continues restoring your setup with these routine notices muted. It is useful when restoring a mode, refresh rate or arrangement is an expected part of waking or reconnecting a display.

See Notifications and Dock for the notification styles and Configuration Protection for what the app restores.