You don't want to use atop, that renders both the black shape with variable opacity that you got from the luminanceToAlpha as well as the source graphic. Instead, you want to use the "in" operator, which only renders the source graphic, but uses the alpha values from the luminanceToAlpha as alpha. You also need to reverse the order of your "ins". This gets you what you want.
<feComposite operator="in" in2="alpha" in="SourceGraphic"></feComposite>