Because shotcut does not support transparency when you remove the second track of the project, you need to export the video in mov to get transparency, it’s just a usual thing, don’t be too frustrated. Shotcut simply does not support transparency until you export as a movie.
P.S:- I was unable to see the video because India has blocked streamable, so we can’t open the site, can you upload the video on vimeo or YouTube and make it unlisted, then send the link, then I can see the video.