I think the cost might be slightly less. I think if you can go for the ATX to get that. It will usually have more options for you also (like ports and stuff)
I'd get the matx if you were building a smaller comp.
Hmm... MATX motherboards are usually the same as an ATX with the exception of 2-3 PCI slots instead of 5 which you probably wont use since pretty much is onboards.
There are several MATX motherboards which allows the same overclocking as ATX motherboards so what are you talking about?
i haven't seen any matx that nice my atx board is top notch with all the beels and wishels and very feature rich bios. the atx is nice to have for those extra upgrades in the future in the end there will be both sides to you question with the choice up to you.