Yes! The mapping between the Document folders is based on Folder name and not the Folder developer name, hence the mapping can be adjusted by changing the Folder names in Source as well as Destination Orgs before starting the migration.
The remaining of Document folders is also helpful in scenarios where you are facing an error while migrating due to special characters in the folder name.
Once the migration is completed, you can choose to change the Folder names back to normal.
PS: View Mass File Migrate Salesforce file migration app on Salesforce AppExchange:
https://appexchange.salesforce.com/appxListingDetail?listingId=e9874a66-2001-4e3d-8a29-3a2ed7f584c4