This issue about transparency and alpha channels has been brought up by @jonray here Can I export as a Quicktime Animation when there are multiple video tracks and maintain transparency?
When you export clips/images with alpha channels, if they are on multiple tracks the transparency isn’t preserved.
If you export each clip/image separately the alpha channel is preserved. I tested @Dr_Pepper_Cans project. Opened each image in the viewer, exported with QuickTime and webm. When the images are opened in SC the transparency is preserved.