As a follow-up, I have decided to RMA the ASUS H87i-PLUS and will be going with the ASRock E3C226D2I (thanks for pointing these out in the previous post) in its place. Unfortunately, its going to cost me a restocking fee and a Haswell Pentium LGA1150 that has never been opened (thanks to newegg's policy). I am going to run the 35w Core i3 in this board that will support ECC and AES-NI. I am going to do a 3-way mirror with 3x3TB WD Reds and extend it later with another similar vdev. 6TB of RAID10 ZFS in an ITX will work great for me.
What it mostly comes down to I've found between the Mini-ITX and Micro-ATX factors is:
Cost: ITX (in a similar board configuration) is more due to the availability of boards currently.
Memory: 16GB vs 32GB capable. (over 32GB takes you to Xeon E5's)
PCIe: additional 1-3 PCIe slots for future drives, NICs, or controllers on an ATX.
A ZFS FreeNAS can be done in an ITX factor, just don't expect to do it on this ASUS board with out understanding the risks.