Yes there’s multiple ways to do that. To do it in Blender, as you described, you can use the white and black as a factor to mix a black emission shader and a holdout shader. Then in your render settings, in the “Film” section, enable “Transparent”. See this image: https://www.dropbox.com/s/cer9feagq70cr5e/clip-art_transparency.png?dl=0
Alternatively, you could render out the black and white image sequence and use it as a mask for your colors in the other software.
