The following code sets a clip on a Rectangle. When the mouse is clicked in the Rectangle, the boundsInLocal, boundsInParent and layoutBounds values are printed:
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import javafx.stage.Stage;
import javafx.scene.Scene;

import javafx.scene.layout.VBox;

import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;

import javafx.scene.effect.DropShadow;

Stage {
    title : "Bounds"
    scene: Scene {
        width: 200 height: 200
        content: [
            VBox {
                var r:Rectangle;
                spacing: 10
                content: [
                    r = Rectangle {
                        width: 100 height: 120 fill: Color.YELLOW
                        effect: DropShadow { width: 20 height: 20 }
                        clip: Rectangle {
                                 x: 20 y: 20 width: 40 height: 60
                              }
                        //translateX: 20
                        onMousePressed: function(evt) {
                            println("boundsInLocal: {r.boundsInLocal}");
                            println("boundsInParent: {r.boundsInParent}");
                            println("layoutBounds: {r.layoutBounds}");
                        }
                    }
                    Rectangle { width: 20 height: 30 fill: Color.GREEN }
                ]
            }
        ]
    }
}

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The result is the following:

boundsInLocal: BoundingBox [minX = 0.0, minY=0.0, maxX=100.0, maxY=120.0,
width=100.0, height=120.0]
boundsInParent: BoundingBox [minX = 0.0, minY=0.0, maxX=100.0, maxY=120.0,
width=100.0, height=120.0]
layoutBounds: BoundingBox [minX = 0.0, minY=0.0, maxX=100.0, maxY=120.0,
width=100.0, height=120.0]

That seems wrong, because the clip should have reduced the local bounds of
the Rectangle.

Now uncomment the translateX: 20 line and repeat:

boundsInLocal: BoundingBox [minX = 20.0, minY=20.0, maxX=60.0, maxY=80.0,
width=40.0, height=60.0]
boundsInParent: BoundingBox [minX = 40.0, minY=20.0, maxX=80.0, maxY=80.0,
width=40.0, height=60.0]
layoutBounds: BoundingBox [minX = 0.0, minY=0.0, maxX=100.0, maxY=120.0,
width=100.0, height=120.0]

That looks correct to me. It seems that if the origin is NOTmoved, the
local bounds and the parent bounds are wrong.