The way iCloud Drive works, if an app registers to use it the system creates the app folder automatically and that folder is the only folder in iCloud Drive that app can access to read or write files. This is part of App Sandboxing security to prevent apps from accessing content they should not be able to access.
As such, I recommend you not mess with or move those folders.
Drafts could, theoretically, allow backups to other locations, but that is not currently supported and has some inherent problems in reliability as access to folders outside the app’s folder requires special permissions be granted, and those can go away sometimes for various reasons and need to be re-granted…which could disrupt automatic backups.
If you are using iCloud Drive for other things and the app folders at the root bother you, I highly recommend you create a folder of your own in iCloud Drive and treat that as the root of your personal files. I have a “Projects” folder I use this way, and just avoid the root of iCloud Drive.