Well, some answers to a bit of testing I have been doing:
I have created a RDM of a 3TB SATA drive connected to the onboard SATA controller, and passed it through to a Ubuntu 12.10 guest VM. I am able to access the entire 3TB, and I do
have SMART capabilities.
Loading the exact same drive into Server 2012, however, is yielding issues. In device manager I see the physical disk, proper model and serial number and everything. In disk management, however, it sees it as a 0MB volume and won't allow me to partition/format it whatsoever. Parted within linux had zero issues with it. I'm assuming this is a 2012 issue, and am continuing to research. I'll likely spin up a 2008 R2 server to see if it reacts similarly.
So in the end, we do indeed have SMART control through RDM without VT-D/IOMMU, but I can 100% attest that setting up individual RDMs for anything more than 1 or 2 drives is an administrative nightmare.
Here is the SMART output from within Ubuntu:
smartctl 5.43 2012-06-30 r3573 [i686-linux-3.5.0-18-generic] (local build)
Copyright (C) 2002-12 by Bruce Allen, http://smartmontools.sourceforge.net
=== START OF INFORMATION SECTION ===
Model Family: Seagate Barracuda (SATA 3Gb/s, 4K Sectors)
Device Model: ST3000DM001-9YN166
Serial Number: Z1F1AAMW
LU WWN Device Id: 5 000c50 04e647ba2
Firmware Version: CC4H
User Capacity: 3,000,592,982,016 bytes [3.00 TB]
Sector Sizes: 512 bytes logical, 4096 bytes physical
Device is: In smartctl database [for details use: -P show]
ATA Version is: 8
ATA Standard is: ATA-8-ACS revision 4
Local Time is: Wed Nov 28 21:03:54 2012 EST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled
=== START OF READ SMART DATA SECTION ===
SMART STATUS RETURN: incomplete response, ATA output registers missing
SMART overall-health self-assessment test result: PASSED
Warning: This result is based on an Attribute check.