I did something similar a few years ago using a OpenGL program I wrote and a Mac with 2 video cards installed on it. Just render the scene as normal to the 1st video card, then render the scene again to the 2nd video card, but this time use no lighting and replace all the materials and textures with white or grays for the desired alpha levels. This way yow will have your matte and fill signals in perfect sync because they are being rendered on the same computer.
I used professional DVI to SDI Component Video converters to output the Mac video signal to the video switcher installed in the control room.
You could also check some of the higher end Nvidia Quadro video cards, some of them have a separate alpha channel output from the frame buffer, this way you just have to render the scene once and the hardware will do the rest for you. I hope this will help