If with high MP's the hi freq noise is best handled with good NR software (it works even after upsamlpling according to Dominique),
and downsampling does nothing to mid and low frequency noise,
than what's the gain in downsampling other than getting a smaller file size ?
Not much. But those were the parameters of the discussion.
Wait a moment.
Downsampling is something that you do routinely to (i) make web sized images, (ii) make prints smaller than a certain size. That one should be able to achieve noise reduction benefits in these commonplaces of photography is good news. That you should be able to aggregate pixels together for purposes of signal optimization is a new consideration to many.
This latter consideration involves a cornerstone of your own teachings -- the notion that for a wide range of pixel sizes, when comparing sensors of equal sizes and with comparable technology, that overall light-gathering ability and noise are more or less equivalent per unit area of the sensor. This figures heavily into decisions about the tradeoff between, say, a 36MP D800 Exmor-Nikon sensor, and a 16MP D4 sensor in a practical way.
To wit: Can the D800 sensor be used to produce high ISO images on a par with the D4? The answer appears to be
approximately yes. But to understand that, most people still need to grasp the idea that when photons are scarce, you can aggregate pixels without any
in-principle penalty in order to optimize signal. In other words, the D800 makes about as good a 16MP camera as the D4 does (modulo considerations about correlated noise, the perception of detail, and work flow).