Firstly, nice write-up up.
VT-d only allows the passthrough of the controlling chipset (ie the LSI 2008 on the M1015 card), not the devices connected to that chipset.
For the M1015 this means that it is all or nothing and you cannot select individual drives.
On another note, some other decent boards to look at for an ESXi build include;
Supermicro X9SCL/X9SCL-F (C202 so only SATA II and less PCIe slots but otherwise the same as the X9SCM-F).
Intel S1200BTL/S1200BTS (C204/C202 ESXi certified boards. BTL has a separate connection for a 4 port SAS controller).
Supermicro X9SCI-LN4 (C204, 4 ESXi supported lan ports on the board but limited expansion slots).
If you want to go small (rare in the world of masses of storage I know) you could look at the Intel S1200KP mITX C206 board (ECC or non-ECC ram, Dual lan - one natively supported by ESXi, PCIe x16 slot - add a storage controller maybe). Should be a fair bit cheaper than the Supermicro mITX boards. Cheaper still, the Intel DQ67EP mITX board supports VT-d and works well.
RB