depends on the board. sometimes they run cooler, sometimes they run warmer. sometimes they dont overclock as well, sometimes they do. often theres a difference in the amount of pci and pci-e slots. sometimes less usb. the vrm cooler might not be as good, might be.
biggest difference of course is size tho. matx cases get pretty sexy but dont have as much room for hard drives and case fans.
Between those boards, the difference is more than ATX v mATX.
The $155 ATX board has better overclockability. Gigabyte often makes mATX and ATX versions of the same board--but these two are not counterparts. Now if you'd be satisfied with a meager 4.2GHz overclock (although it probably can go higher), go with the $115 mATX board. Then you can spend the extra on graphics. It's SLI/CFX compatible, so you're good on that.
If you expect a 4.7GHz OC out of your machine, you should probably spend a couple more bucks. But if your purpose is gaming, more than 4.0GHz with an i5-2500K isn't gonna keep you under 90fps on any games--and your monitor can probably only do 60fps.
EDIT: Btw, make sure your case has solid cooling if you plan on dual card configurations.
What are you planning on doing with that system? There's a chance I could save you from wasting a bunch of money. For example--starting out with dual cards is often not the best choice. Also, an i7-2600K doesn't game at better framerates than an i5-2500K.
You're getting the non-SE GTX 460 1GB cards? I guess if you picked those up on the $100 deal a couple days ago, that's a great deal--Although I'd still take a single GTX 560Ti for $183 over dual GTX 460 1GB's for $220 (since only one will get the rebate to make it $100).
Make sure your PSU is a good one. That means Antec, Corsair, Seasonic, or XFX. (There are some other brands that cost more or tend to be good, like Silverstone, Enermax, or PC Power & Cooling, but me saying this will just complicate things unnecessarily). You'll probably want a 650W one--XFX had a good one for $49.99 after rebate last month.