I have tried setting up a mount point on a DFS share in a test environment (2008 server R1), mounting the volume directly in/on the replicated folder.
After starting and verifying the replication I brutally removed the volume from the mount point to see what happened, and DFS basically seemed to think that I'd deleted all files, and removed them from the replicating partner as well.
The question is if 2008 R2 is more aware of mount points, or if Microsoft is planning to implement it in any future releases. Insight is welcome!