This is a fairly common problem. Unfortunately, however, I'm not aware of any fix to prevent the initial creation of the duplicates, short of using the "move contents" option. There is a 'workaround' for this issue, but first I should mention that you don't need to keep the "move contents" option turned off all the time. If you only need it off when you migrate data betweem servers, then only uncheck when you're migrating data, and turn it back on afterwards. This option can be changed at any time - you're not stuck with it in whatever position it was when the folder was created.
Otherwise, your best approach is probably to handle this from a cleanup perspective: I would use Group Policy Folders to remove the duplicates. You could configure one item per folder as shown below and apply the policy to all new users.
Pro-tip: While this will fail gracefully if the folder doesn't exist, it'll log a failure to the event log every time it runs. You can prevent a ton of event logs by either use the "Apply once and do not reapply" option, or by using item-level targeting to prevent the policy from running if the folder doesn't already exist.
Another possible answer is using automated profile cleanup. If and only if you use roaming profiles (and you store cached copies on clients), you can configure the client systems to automatically cleanup (remove) profiles that haven't been logged on to in a specified period of time. You could specify a very short time period, forcing all the profiles to be cleaned up. Since the duplicate folders are local folders only, they would not reappear when the profile is re-downloaded.