Another major difference is electronic shutter (KAI 4020) vs Mechanical shutter (KAF 8300). The electronic shutters are easier to use when taking flats etc, the mechanical shutter needed for the full frame chips can leave artifacts if you dont have your timing down pat. The electronic shutter is also better for very short exposures like the moon and planets (I would not even try with the KAF 8300) but full fame sensors are better for AP even with the extra complexities introduced by a mechanical shutter. This makes a good read on the differences.
http://en.wikipedia.org/wiki/Charge-coupled_device
The KAF 8300 does have 1000x blooming protection whilst the KAI 4020 has 300x but you would expect this when well depth is 25000e vs 40000e respectively. I have not used the KAI 4020 but the KAF 8300 is pretty clean noise wise at temps below -20 C. The KAF 8300 is cleaner with 16e Vs 25e total noise for the KAI 4020. In short the noise performance is going to depend on the camera you buy. The deeper the cooling the cleaner the result. Good cooling and darks go along way towards minimising noise.
Mark