For RenPy it uses the notion of an Alpha Mask video https://www.renpy.org/doc/html/movie.html#movie-displayables-and-movie-sprites
I can convert the a bunch of PNGs with alpha channel to http://wiki.webmproject.org/howtos/convert-png-frames-to-webm-video I was wondering how to do the same sort of thing without creating another set of PNG files with just the alpha frame.
I'll be okay with something that uses imagemagik in the middle if needed.