It might be that looks are deceptive and there may be no issues in pracitice, but i have noticed that lots of mini-ITX boards have the CPU socket near the bottom next to the PCI-E lane.
If you were to install a decent air cooler, and a graphics card at the same time, would this not create certain space issues?
If you were to install a decent air cooler, and a graphics card at the same time, would this not create certain space issues?