Hi
So about the two relationship. i didn't try it - and never worked on Cdot sync volumes. However, reading in the docs, you are allowed to snapvault from the source, and allowed to cascade the dst to snapvault. so i assume you can have two relationships going to the 3rd cluster. Having Aggregate level deduplication - will assure that you minimize the space loss of having the duplicate dataset.
As for the failover scenario - for my understanding, you will maintain the original reference snapshots on each Sync volume regardless of it's state (broken, reversed or active)- so you should be able to resume the snapvault at any given time from both volumes once they are online.
As for ONTAP select, this is ONTAP virtual machine running on VMWare, but can be stored on your physical ONTAP. it was just a long shot idea, along with the Windows/linux VM in case you already have the virtualization and backup facilities.
Now thinking on this all - I really suggest taking it to NetApp/partner, and see what they see the best option for you. I'm pretty sure a 3rd party will need to be file based, and i agree with you this is not ideal at all (for the backup itself - and more important for a restore) .