The BlendEffect an accomplish a chromakeyed video overlay. I don't have the exact code for it at the moment.I tried using blend effects to accomplish this and failed pretty miserably at it. I thought I would be able to use the BlendEffects to create a stencil of the video which could be used to either selectively add alpha in to the areas required or be used as a binary image mask (http://en.wikipedia.org/wiki/Image_mask#Image_masks). But the Blends did not seem to support the range of operations required to do this. Not all of the awt alpha compsiting operations are available as blend modes in JavaFX http://docs.oracle.com/javase/7/docs/api/java/awt/AlphaComposite.html.
If your input video can be preprocessed in an external tool to include an alpha channel on the areas where you want it to be transparent, then I think it should be trivial, just play your video using the MediaPlayer and the background should show through the transparent or translucent pixels in the video.So I tried this and it worked :-)