An '/uploads/' folder can contain anything at all and the database does not ever care as long as it knows what info to give WordPress in order for an upload to be displayed whenever requested by a browser. And so, the question here is this:
Can and/or how can a single upload be registered in more than one database?
'Add From Server' is a plugin that can properly register uploads in a database so the database can know what info to send to WordPress, but I do not know how 'Add From Server' will act if something such as '$ROOT/uploads' is at work in wp-config. Also, and even if that does work, I do not know how WordPress would act during the registration process instigated by 'Add From Server' if the upload being registered already had its corresponding thumbnails in place as done during a previous registration in a different database. Also, it is logical to believe both sites would first need to have identical settings related to thumbnails and cropping.
I think it would be safe to try the above to see what happens, but I have no idea what the end result would actually be other than to say there is no reason to believe a previous registration in a different database would be corrupted.
edit: If you do give 'Add From Server' a try, you first need to do the upload manually via FTP/SFTP or whatever, and then use 'Current Time' rather than 'File Time' within 'Add From Server'.