Region ignores any transforms set in Shape set Region#setShape()
Testcase:
@Override
public void start(Stage stage) throws Exception {
Region region = new Region();
region.setBackground(new Background(new BackgroundFill(Color.RED, null, null)));
final Shape shape = new Circle(30);
shape.setScaleX(2); // IS THIS GETTING IGNORED ?
region.setShape(shape);
region.setScaleShape(false); //lets make this obvious
Group group = new Group(region);
region.setLayoutX(100);
region.setLayoutY(100);
region.setPrefSize(100, 100);
Scene scene = new Scene(group, 300, 300);
stage.setScene(scene);
stage.show();
}