If I knew I was building an ATX case I would use an ATX board.
My reasons.
1. You can space out the cards you put in for better airflow
2. You never know what you might want to add later. If you already are using a discrete video card and a discrete sound card then 2 of the four slots are full. If you were to throw in a Ceton tuner your PCI-e slot would be goen and now you are already down to 1 and each cards is pretty much on top of the other.
3. I potentially see a USB 3 card in my future also.
