I started questioning my recommendations and went looking at even the cheapest of the cheap mobos and haven't come across a H97 or Z97 chipset that doesn't have options for Intel Virtualization Technology... I'm not saying there isn't one that doesn't support it, and I'm not going to peruse through 100 manuals to prove the theory... but I didn't find one...
http://pcpartpicker.com/p/hGsmNG
That'd get the job done... and yes it supports it as well... ftp://66.226.78.21/manual/Fatal1ty%20H97%20Performance.pdf
http://pcpartpicker.com/part/asrock-motherboard-h97mpro4
That also works if you want a Xfire capable mATX board that supports VT-D... at well underneath your budget...
if you just have the $400 already set aside and want to use it all, I'd look at something along these lines...
http://pcpartpicker.com/p/74Qyqs
few dollars over budget for the flexibility of being able to overclock (and an iGPU you won't use)...
Generally with a full ATX board, you're getting better VRM cooling and more PCI lanes... yes, your case will be bigger, but that also makes it easier to work in and in general has better airflow... AND if you're going full ATX you could look into a 990 chipset and a FX8320 at a good bit less than the price of a Xeon/H97 option... just don't buy the cheapest motherboard you see for an AMD 8-core...
AMD option:
http://pcpartpicker.com/p/dp27P6
the 8 cores are great for virtualization, they just don't make decent motherboards in small form factors... the downside to AM3+ is that it's a dead socket which leaves you with no upgrade path... if you plan on playing CPU-intensive games like ARMA3 it also has it's limitations there... excellent choice for A/V processing outside of Adobe suite, which seems to be optimized for Intel... It IS a 3 year old platform, and in general vs. a Xeon or i7 will show it's age in benchmarks, but it's fantastic bang for buck with virtualization in mind and I've heard a lot of Linux users prefer them... of course all AMD processors are unlocked and can overclock...
To directly answer your question... you're not pushing any limitations going with mATX, you're just limiting your PCI lanes which you seem to be fond of, and are forced into Intel for decent computing power... hope I helped :)