You raise a good point that I had not considered. In my previous test, I minimized falloff by using f/8 with a 105 mm lens. I repeated the tests with the Zeiss Distagon 21 mm f/2.8, which is an excellent lens but is known to have considerable falloff. Rather than upload the large raw files, I chose to merely show the results. However, the matrix metering results in lower saturation in my tests.
I have a different method of demonstrating the falloff effect. I set the camera on a tripod to photograph a gray card, and then I take 4 images. The first two, Spot and Matrix, are with a light source very close to the card so that the card exhibits falloff. The second two, also Spot then Matrix, are with the light source moved further away to minimize falloff. The result is that my first two images have different exposures, but the next two images don't...even though the only change to the camera, between the images of each pair, was the metering mode. So that demonstrates that the falloff is affecting Matrix metering.
However, in my shots with the light source close to the gray card, the Matrix image is clearly brighter...which, to me, would be the expected result of a metering mode that is averaging dark areas with bright areas. So I don't know why you got the opposite result. I've put the NEF files on my FTP...ftp://graystar.tftpd.net
(this address has to be copied and pasted into the address bar, as the forum software is adding an "http://" in front of it.)
DSC_9310 - light source close, Spot (f/8, 1/640s)
DSC_9311 - light source close, Matrix (f/8, 1/400s)
DSC_9312 - light source far, Spot (f/8, 1/20s)
DSC_9313 - light source far, matrix (f/8, 1/20s)
EDIT: The only time you get standard exposure from Matrix is when Matrix fails to match a scene in its database. Just wanted to note that with the D800's expanded scene database, it's possible that Matrix found a match between your image and one of its scenes, and applied the exposure compensation related to that scene (this is what makes Matrix so unpredictable.)