It's all about the GPU length. When you start looking into high end GPU's they actually tell you the length on them specifically so you can double check that you have enough clearance in your case. Both the Radeon HD5790 I had originally and my new R9 290x's are extremely long cards.
Here you can see why I had to originally use my PSU externally; note the bottom right side is where the PSU would sit in this particular case design, you can see where I had to cut into it a good 3/4" to make this card fit (In this picture the front of the case is on the right side):
That's actually why I switched cases when I got the 290x's because they're even longer. The SilverStone case is awesome because it's got the PSU along side the motherboard instead of in the front of the case (In this picture the front of the case is at the bottom)
As for why I went with these particular cases, sheer aesthetics. I wanted a to have it look like a stereo shelf rack system: (from the bottom in the picture is my home theater receiver, my bottom case, and my top case. That's a custom built shelf that connects up to my desk):
TMI FILE:
Its a completely customized system or fully "modded" as they say in the custom computer world; I popped the entire back off my top case and refabricated the back in order to center the MB so that I can run water pipes along both sides and not have it look off center. (Original case back, and centering the MB in the case)
Newly modded top case (you can see the water pipe fittings and such in the front of the case, you can also see that these GPUs overr hang the MB by a good 2" at least heh (front of case is on the right side in these views):
As I noted I centered the MB so that I can run pipes to my CPU and GPU's on either side of the MB and I moved all the "guts" (the PSU and drives) in to a second case so that I can put a reservor in the front of my top case. (First one has my LED mb tray I made, and the second gives is a mockup with a reservoir [though not the res I'll be using in my final design] also the cards will be a bit shorter without the shrouds when I switch them over to watercooling - waiting on a part for my new res) There's an aluminum panel that goes on the front in the third pic, holds the res:
(this is my new res):
Also, my LED tray is set up so I can completely customize it's color, flashing, etc. I've made my own audio driver PCB (kind of like a motherboard) to run the LED's in time with music if I feel like it - here's a little video of third round of testing as I've fine tuned the lights on the MB tray to flash with the bass of songs [the middle box at the top in the beginning there was my second led test as a reference to show how much I've been able to fine tune it to the base driver]) -
LED test
I've made separate PCB drivers for LEDs that'll be in the water pipes on either side of the motherboard as well as LED's that'll be inside the reservoir, behind my monitors, and behind my guitars and violin that hang on the wall - they're all connected so that I can swap the auto channel (right, left, center, rear right/left, sub etc.) to any of the lighting sections I want. So essentially I can do anything I want with my lighting in the room (which I wanted for my singing videos - this system will eventually be in a recording studio upstairs after the last of the kids moves out in a few years.)
Finally, for GP, this is my second (or bottom case) with the PSU and drives in it. I've also got an Asus AM1 ITX down there; basically a small PC where the cpu and graphics card are combined on it. (like a laptop or a tablet in a lot of ways) I use it as a coding platform [I'm a programmer] as well as a juke box)
I also do 3D rendering for architecture which takes a beefy card as well. I make videos also so a lot of graphics processing needed. Its a recording studio, a 7.1 surround sound theater, and an all around beauty 
