shape.setClip(Path.intersect(shape, shape1)) and shape.clip(shape1) should return the same result.
 
Take a look at attached file and run it, please. Or just take a look at the picture first.
Pictures in the first HBox are onle examples. Picture in the second HBox is result of .setClip(Path.intersect(shape1, shape2)) and the picture in the third HBox is result of just .setClip(shape2). Why are they look so different?
The result of just clipping without intersection looks much more logical.