I have 1 client that loves everything about the WP Media Folder except when we sync to S3, we don't want the database URLs to rewrite to S3. We are not trying to use this feature as a CDN but rather a real-time sync/back-up system. Specifically for large podcast MP3s.
A normal backup system would zip the uploads folder and send it off once a month or so. That is horrible for space/cost and server performance when you have lots of large mp3 or mp4 files. A better solution is to simply sync them to a cloud site for safekeeping.
In this case, we are not trying to use the S3 URL for distribution because the server already has great speed/distribution CDN in place. We just want a backup in case anything ever goes wrong.
On the cloud options admin page a toggle to "do not rewrite wordpress urls during sync" would be perfect.