Some ShareCenter owners have used 2 TB (max size) HDDs with SmartAlign in Standard Configuration, but I would be very cautious about using these HDDs with RAID (of any flavor), and there have been no posts regarding the long term stability of these HDDs in "any" configuration (RAID or otherwise).
Unfortunately, there is no firmware version that explicitly addresses Seagate SmartAlign, by name. The only reference from D-Link regarding handing of non-standard HDD formats is "Advanced Format" in firmware beta v1.05b01.