Windows server 2016 dedupe actually brings lots of major enhancements to deduplication and really becomes interesting... There are still limitations compared to hardware dedupe boxes but that is expected
Anyway, I would chose backup storage (I still need to start testing the moment v9.5 releases...) but in the end, it really doesn't matter what you choose.
General files gives you these options:
- Background optimization
- Default optimization policy: Minimum file age = 3 days, Optimize in-use files = No, Optimize partial files = No
Backup option gives you this:
- Priority optimization
- Default optimization policy: Minimum file age = 0 days, Optimize in-use files = Yes, Optimize partial files = No
- "Under-the-hood" tweaks for interop with DPM/DPM-like solutions
The only one I personally would be scared off is that "under-the-hood" tweaking as I have no idea what it does for the moment. But, if you take the general setting, then you can easily change all of these options by using PowerShell or mostly in the UI also.
So you can start with the general files, and then tweak it to the same settings as backups (without those under the hood tweaks
Hope it sheds some light