The vp9 sample you provided has pixel format yuv420p, which does not include an alpha channel. If it did, it would say “yuva420p”
(nor to export any movie containing alpha)
This is advanced usage of Shotcut. There is no way to remove the black background in the Timeline, but you can work on a purely clip-based project and export it. After importing your webm and applying a chroma key filter to remove the black, you can export it with alpha by:
- go to Export
- choose your clip in Source player from the From dropdown
- choose “mov” from the Format dropdown
- click the Video tab
- choose 'qtrle" from the Codec dropdown
- click the Audio tab
- check Disable audio
- click the Other tab
- add “pix_fmt=argb” to the Other text box
- click Export File
This creates a Quicktime Animation, and there might be a way to output other formats with alpha, but this works.