Motherboard rotation and GPU cooling

I am planning to build a new case from scratch using oak and aluminium. I've been drawn towards the idea of mounting the motherboard with the I/O at the top (like a Silverstone fortress or raven), as it means I can place the PC flush against the wall, and I think it makes cable management easier. Doing some research, I came across a thread (few years old) that said GPUs with non blower style coolers would perform poorly due to the orientation of the heat pipes. I'm looking to buy an AMD R9 series card, and I certainly don't want to have that noisy stock cooler.  Does this problem still occur with more modern graphics cards? Would this really be an issue? Has anybody had any experience with this problem? Would the MSI twin frozr, Asus dcu, or gigabyte wind force cards be effected?

Thanks in advance.

I did a little bit of digging around and found out that orientation doesn't really have too much of an effect on heatpipe's operation because they rely more on thermal convection than gravity. Have a little read of this http://www.overclock.net/t/1104066/brief-study-on-the-effect-of-heatpipe-orientation-in-cooling-efficiency

If you're worried about the slight (really insignificant) temperature rise caused by orientating the card with the heatpipes vertically, then try designing the case so that you could use pci-e risers to mount the cards in a normal orientation.

http://www.quietpc.com/nof-cs-70

Eww...