You need to also note that there are kind of advanced controls for the files when you edit a submission.
For instance my Trijam 266 submission had a platform problem that I just needed to update one thing. So in the edit screen there are several options for both zip files. I could do many things, including delete, either or both of them.
I do wish there was an archive option, like versions that are still playable but the casual player doesn’t need to worry about.