downsampling to reduce noise - how much?

http://blog.dpreview.com/editorial/2008/11/downsampling-to.html

Phil's results look wonky, no doubt because he used jpeg and noise reduction at some point in apparently every workflow in the test. And I see (surprise!) the blog doesn't allow comments. What are we going to do with you, Phil?

Averaging pixels 4:1 obviously increases the number of photons collected per-pixel by a factor of 4, so the shot noise, sqrt(n), goes down by a factor of 2, so the SNR goes up by about 3dB or 1 f-stop.

But that's per-pixel noise. It's even more obvious that, since sensor sizes aren't changing, the average number of photons collected per-image is constant from generation to generation. So more megapixels just give the photographer the option of extended resolution when plenty of light is available.

That is, assuming photosensor boundaries don't take up much room, or restrict the angle of effective incoming light. Which I think they do. Microlenses can compensate, but no doubt introduce their own transmission loss. Anyone have any information on this?