Right, one of us may have misunderstood.
The black background in the sequence preview isn't "real", it's just what the video is displayed against. There's no need to use the "blank clip + green screen" method, as there's nothing to remove.
Unfortunately, VideoPad doesn't support encoding alpha into the .webm format at the moment. The only way currently to achieve this in VideoPad is to export to a .gif, but that sounds like it may not be useful to you. (There's also Image Sequence export, but that sounds like it would be even less useful to you).