Node.setMouseTransparency only works if there is not fill, no border, no shadow or any other visible element. It is not possible to create a transparent window with a translucent fill or a no-fill shaped with a colour border or even a shadow that a user can click through to the window behind.

The problem with shadows is particularly unintuitive because a shadow is supposed to be the absence of light cause by a nearby visual element. It shouldn't behave as if the bounds visual element extends to where the shadow is. Real life shadows don't behave that way.

This RFE asks for a method to allow mouse transparency on visible elements on a transparent window.