I suggest giving Admins the ability to enable or disable system generated notifications. These notifications are, for example, grading policy changes.
We heavily use blueprints, and when an update was made to the weights of the assignment groups in the assignments page a system generated notification was sent to students causing all kinds of confusion for them. If we would have known that updating the assignment weights would have sent a system generated email to the associated shells we would have thought about it twice before making the change. Changes to blueprints are necessary for our organization and there's no way around that.