I'm not sure I understand what you mean by it created separate folders. A split zip wouldn't be a single file.
For an example of what I mean by split zip, this game uses it for the downloads: AI Roguelite 2D by maxlohmusic
Edit: after testing, that game won't install through the itch client so I guess that wouldn't work anyway. Not unless itch updates their client to work with split zip files. But that's unlikely. They haven't updated their client in years as far as I know.