GPU/CPU cooler sandwich or use the 8x PCIE slot

hi all,

im currently in the process of building a micro ATX build with slightly older component. I have an ASUS strix Z270g Gaming MATX, a GTX 1080 to go in and a Thermalright Peerless Assassin 120 SE cpu cooler already installed.

The issue I have is that if I test fit the GPU in the 16x slot, there is about 1-2mm of clearance between the bottom of the cooler and the faceplate of the gpu.

i have an 8x slot on the motherboard that I can use for the GPU, which has a much better clearance from the cooler, in turn leading to better thermals, but could this significantly impact the speed that the gpu runs at?

obviously I’d rather have a happier and cooler GPU and that being said the gap just seems to tight, but has anyone got any advice which option they would go for and why.