It's like that so that the ledge where you screw down the graphics card or other PCI cards is not sticking out. On the cases that are not recessed like that, that ledge for extension cards will stick out and the screw there will be on the outside.
I'm trying to wrap my head around that config. The motherboard is on the wrong side and upside down, but the ports are still at the top. I'm guessing it's some kind of prefab but even they usually follow standard layouts.
Edit: I guess it's a BTX system. I didn't know those were still around.