Regarding the change from a side panel with a mesh vent to a window, I am not sure if this would make much of a difference to GPU cooling. I have the original Fractal Midi and I wanted to isolate noise a bit more, so I swapped the side panels so that the vented one is on the back of the mother board side. I had also installed 1 extra 140 mm fan in the bottom of the case blowing up to draw in cool air underneath. I did this before swapping the side panels. All of my 140 mm fans are turning at 700 rpm. Surprisingly I noticed that in this configuration the GPU was slightly cooler (1-2 C) at idle and under load with the solid panel on the right / GPU side, and the noise seemed a little lower. CPU temps did not change. I would have to guess that the mesh hole provides an escape port for air and the GPU fan has to work harder.
Heat Sources: i5-3570K @ 4.4 GHz, Hyper 212 EVO, EVGA GTX 560Ti @ 900 MHz, 3 WD Cavier Black HD