I'm digging "old" thread just to add some infos.
For those saying to activate per-vm on deduped windows volumes, I would advice not to do so. I think windows get lost when there is too much files because I faced this problem and once it happens, any optimization job will faill with "exited unexpectedly" even after full GC and scrub jobs that went successfully.
On the other hand, never got any problem on another deduped volume which do not have per-vm backup file split, dedupe works great and my files are like 4TB.
Also about win2016, I don't think the story about only first TB processed is true, you can check yourself using Measure-DedupFileMetadata cmdlet, check DedupSize and DedupDistinctSize values, on a folder with multiple deduped files over 3, 4TB (cmdlet is slow to run, but it is supposed to count every block of every file in the folder, so...)