If you look at the mechanical drawing of the schematics of the design (on the page you linked to), the hardrive is under the 3.5 bay, next to, but not over the motherboard. The 5.25 bay hangs over part of the motherboard, over the PCI/AGP slot area. That's why I said to get a fully integrated board like the NV7m, or another nForce board, or one based on the Intel 845G/GE chipset. So, you won't need to use any PCI/AGP cards. If you look at the design of the case, if you wanted to use PCI/AGP cards, you'd need half-height cards anyway.
So, if you don't have any cards, the tallest part of the boards in that area will be the empty PCI/AGP slots, which are less than 1.5 inches. So, you should have no problems fitting a DVD, and hard drive into the case, with a 9.6" square mATX board.
But don't quote me on that. I had problems fitting a mATX board into a small ATX sized mini-tower case (the case was not too deep, and the CD-ROM was interfering with the memory slots).
Ask the guys at Directron if they could take a look at the case, and see if a 9.6" square mATX board, DVD player, and hard drive can fit in it with no problems.