I figure that it's probably that at 41MP, there's tons of noise, but using those 41 MP as oversampling and resampling it to 5 MP (which appears to be the default and suggested setting), it gives superior low-light performance (as he demos in the video with the pictures taken at midnight)
edit: at 2:30 he says "It's not about putting loads and loads of megapixels into a device, it's about how you use them"