That slot is a holdover from days when a PCIe x1 slot lived atop the first graphics card slot.
To install the GPU, you'll likely have to remove some slot covers on the back of the case so that the DisplayPort, HDMI and any other graphics card ports show through, letting you connect your monitor(s) later. It's a good idea to first try lining up your card in the case alongside its slot before installing it, if you want to save yourself the hassle of removing the wrong brackets and having to re-install them later. Usually, the top expansion bracket will not have to be removed. That slot is a holdover from days when a PCIe x1 slot lived atop the first graphics card slot. But these days that area is now occupied by the primary M.2 connector (often hidden behind a heat spreader).