I'm not sure if this helps, but its a single pixel that is sub divided. It was not intended to act as two separate pixels, due to the geometry.
As others noted, the Bayer Filter covers the entire pixel with one color.
Here is a schematic diagram of the photosite from Canon's Patent Note that the tops of the two sub pixels are slightly angled so they pick up light from different directions. This geometry allows for the phase detection AF, but they need to be combined to get light from all directions.