Acronis Files Connect (formerly ExtremeZ-IP) uses alternate data streams (ADS) for storing Mac specific data (resource forks). Files that contain ADS will not be deduped by Windows Server 2012 and 2012 R2 Deduplication (see the linked Technet article, below). While a Customer could still use this technology on the server storage it would not provide the same benefits for files that are accessed from the Macs. It is also important to understand that in the Mac OS X 10.7 SMB client (and later) Apple uses the same ADS formatting that is used by AFP with Acronis Files Connect. In this respect there is no better alternative that is native to the Mac.
It is also the case that we have not tested this feature of Windows 2012 and 2012 R2 and do not officially support it. It is very likely that it will work without issue, but again there will be no deduplication of the files that are used by Mac users.