Prototypes are declared when object is defined. When it is instantiated, it does nothing related to prototypes in KineticJS, afaik.
To redefine the prototypes of objects, you can run the following again to add additional prototype of Kinetic.Node.
Kinetic.Global.extend(Kinetic.Container, Kinetic.Node);
Kinetic.Global.extend(Kinetic.Shape, Kinetic.Node);
Kinetic.Global.extend(Kinetic.Group, Kinetic.Container);
Kinetic.Global.extend(Kinetic.Layer, Kinetic.Container);
Kinetic.Global.extend(Kinetic.Stage, Kinetic.Container);
Kinetic.Global.extend(Kinetic.Circle, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Ellipse, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Image, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Line, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Path, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Polygon, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Rect, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.RegularPolygon, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Sprite, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Star, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Text, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.TextPath, Kinetic.Shape);
Kinetic.Global.extend(Kinetic.Wedge, Kinetic.Shape);