Backing up the file/folder structure on a DFS share doesn’t work, and backing up DFS through the shadow copy components is painfully slow, so I directly backup the DFS share.
The DFS configuration is backed up when I backup my domain controllers. The configuration and the data are all I’m concerned with backing up, so half of that problem is already solved for me. I back up my data by creating my selection list at the share level instead of at the file structure/folder level and exclude the DFSRPrivate folders in each share, as they won’t backup anyway. The disadvantage of this approach is that I won’t have any of the queued replications, but the advantage is that I get a backup in 2.5 hours instead of 14 hours. Half of my remote sites are configured to replicate to this DFS server and the other half will be configured to do the same soon. This means I’ll get a full backup of my remote sites in 5 hours instead of 28 hours, which would take me outside any reasonable backup window.