Use
ffmpeg -i video.mp4 -filter_complex
"[0]split[m][a];
[a]geq='if(lt(lum(X,Y),16),0,255)',hue=s=0[al];
[m][al]alphamerge,format=yuva420p"
-c:v libvpx output.webm
Veja aqui sobre como use este arquivo no Chrome.
As of now, VP8 alpha playback is behind a flag, so you have to either enable it in about:flags or set the command line flag --enable-vp8-alpha-playback when you start Chrome. When the flag is enabled, alpha playback also works with MediaSource.