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. Mute these notices if restoring a mode, refresh rate or arrangement is a normal part of waking or reconnecting your display.

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