Adam,
One of the most endearing things about a William Flynn course (at least the three I've played: Manufacturer's, Huntingdon Valley, and Rolling Green) is that he seemed able to route the golf course to attack and use the distinguishable features of the site in many different ways.
At Manny's, Flynn used Sandy Run to gaurd 4 greens (2nd, 5th, 10th, and 17th), and at a cursory glance the usage of the creek looks redundant. However, a closer look shows that the angle of the creek in relation to the green, the distance from the creek to the green, and the appearance of the creek and green from the fairway all vary and all enter play differently.
He used the quarry and deep swale on the site in similar ways: varying angle and distance from the target to fool and tempt the golfer.
Is this too much of a good thing? In this case no: but a different architect on the same site may have abused the site's natural features.