The four-pin RGB headers are for use with the 5050 style RGB lighting systems. Those pins are a common +12 VDC supply line, and three Ground lines, one each for the three LED colours in the system, and controlled by the mobo header - connection of a Ground lead to an actual Ground lights that group of LED's.
The 3-pin RGB headers are used with Addressable RGB lighting systems. Although the header pin layout looks similar, as OP has found one of the holes in the connector is blocked off so you can NOT plug it into a 4-pin header by mistake. In that system, 2 pins are for +12 VDC supply and Ground. The third pin carries a control signal from the header to an actual controller chip in the lighting device, and that is what controls the lighting effects in that unit.
The ASUS Aura Sync system is a means of motherboard control of LED lighting effects via software, and can be applied to either type of RGB device. The "trick" is that some of their motherboards have only ONE of those two types of headers on them and thus can be used only with that particular type of lighting device. Other ASUS mobos come with BOTH types of headers, so you can use either or both types with that mobo design.