Guest vs. host dedupe

The dedup ratioos will be different as one is backup up the VHD files (using a stream handler and then doing a GRT operation) and the other is backing up the data within the file system of the VM (so inside the VHDs) using a nromal file system dedup operations.

Because at any point in time all sorts of random changes could happen inside an active VHD I would expect the vhd not to deduplicate as well although the exact ratio difference would probably be difficult to predict and I am therefore not sure that the values you quoted are expected.

That said if you do only agent based backups of data inside a VM, a full DR operation would be more complicated that tha doing the VM itself. There may also be performance gains for both backup and restores.

As such even with the decrease in dedup ratio you might still want to do VM backups because of the other advantages.