If you zoom in on the image of the board on newegg you can see that the 3rd and 4th slots are labeled x4 and x8 respectively.
yeah that's too bad since they have that board at microcenter too: http://www.microcenter.com/single_product_results.phtml?product_id=0364087
It's too bad but I think I'm just going to go with the stock cooler. It will keep the i3 and components cool and if I put a VGA card in that will seperate compartments anyway so it shouldn't harm airflow in the GPU region anyway, which is the trickier component to cool. The top-down cooling will make the side fans work a little hard but I can probably keep it cool with the fans at minimum voltage anyway (here's hoping!).
The biggest concern is the noise of the stock fan, in which case going with the Silverstone NT07 *might* be a better option, I don't know if anyone has experience with that.
I will call silverstone this week though to express my frustrations over this issue, because they recommend
using the NT01-E with this case without making any mention of blocking the first slot position, and indeed the picture on their website (now taken down, but can still be found posted elsewhere) with the NT01-E in the GD04 makes it look quite clearly from that angle like the slot is clear, only if you notice the shadow of the bar in the zoom in can you tell that it is a perspective issue and that the slot is indeed blocked. If there are any silverstone reps online they should take note