I can tell you have never designed a CCD sensor. The thing is, A CCD is basically a large array of photo capacitors. You chain them together so when a photon hits one of the capacitors, it charges all of the ones on that block. each block has one cap that has additional circuitry allowing it to be read. This is a good thing because, the more capacitors you have linked, the bigger the individual physical pixel is and the lower light it can operate without noise. If you design the system to bin pixels, you must allow pixels to be able to electrically link and unlink. This requires quite a bit of additional wiring and it must be done at the pixel level.
One of the key design goals of creating a CCD chip is to minimize all the parts that don't directly gather light and turn it into a charge. Everything else is parasitic.