Albert Theuwissen publishes a blog post explaining a difference between different ways to bin pixels and average them:
"Conclusion : charge domain binning is more efficient in increasing the signal-to-noise ratio compared to binning/averaging in the voltage domain or binning in the digital domain. The explanation of binning and averaging as well as the discussion about signal-to-noise ratio in this blog takes into account that the noise content of the pixel output signals is dominated by readout noise. The story becomes slightly different is the signals are shot-noise limited. This will be explained next time."