Node.getBoundsInParent returns some very expected results when node has rotation applied. Here's a code snippet I created to reproduce the problem.

The values of boundsBefore and boundsAfter should be the same but the height and width for boundsAfter is a much larger value while boundsAfter.depth remains 20. This seems related to the rotated axis, Z.

Sample code (using Cube3D sample from netbean):

public class Cube3D extends Application {

    @Override public void start(Stage primaryStage) throws Exception {

        Group root = new Group();
        root.setDepthTest(DepthTest.ENABLE);
        primaryStage.setResizable(false);
        primaryStage.setScene(new Scene(root, 400, 400, true));
        
        PerspectiveCamera camera = new PerspectiveCamera(true);
        camera.setFarClip(200);
        camera.getTransforms().addAll(new Rotate(-30, Rotate.X_AXIS), new Translate(0, 0, -100));
        primaryStage.getScene().setCamera(camera);
        
        Sphere sphere = new Sphere(10, 1000);
        sphere.setMaterial(new PhongMaterial(Color.ORANGE));
        root.getChildren().add(sphere);
        
        Bounds boundsBefore = sphere.getBoundsInParent();
        sphere.getTransforms().add(new Rotate(45, Rotate.Z_AXIS));
        Bounds boundsAfter = sphere.getBoundsInParent();

        primaryStage.show();
    }
}