What you're seeing is most likely the result of variability in the experimental conditions.

Almost all the DXO mark scores relate to noise in some way. Dynamic range is measured by finding the difference in illumination between the saturation and the point where the signal to noise ratio drops to 1. The colour sensitivity score is the logarithm of the number of colours than can be distinguished, two colours are "considered distinguishable if their difference is larger than the noise". The low light score is the amount of gain that can be applied whilst retaining a certain signal to noise ratio, thus all three of the scores you mention are determined by how much noise the sensor is producing under certain circumstances.

Noise is influenced by the temperature of the sensor, which depends on how long the sensor has been active for, and the ambient temperature. Anything and everything could have affected the test results, including the weather.

There's also a smaller possibility of sample to sample variation in sensors. Or more likely batch to batch variation - Nikon will probably produce a thousand D800 units, then change over the filters and make a hundred D800E units then change back. So even if you compared two D800s and two D800Es you might find the same result.

You could also be seeing the variable effects of sensor calibration, there will be some steps performed on the production line to set the appropriate black level, amp power etc.

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I see no reason to expect dynamic range or colour sensitivity to be any different at the image level when using a camera with the AA filter cancelled out. The AA filter is not removed in these cameras, instead the two parts of the filter are aligned differently so they have no overall effect. Therefore light passes through exactly the same amount of exactly the same materials in either case. The only difference between cameras with an AA filter and those "without" occurs at the pixel level.

Optics cannot reduce noise (except by delivering more light), neither the AA filter, nor diffraction nor a soft lens reduce shot noise at the image level. With an AA filter, each photon will at random land on any one of four pixels.

I say at the image level, because a single point of light shining through an incredibly sharp lens will result in four noisy pixels in an AA camera image, but one less noisy, brighter pixel in an AA filterless image (on account of collecting 4 times as many photons). However by time you add up the effects for all points of light across the image, the results cancel out and you're left with the same overall level of noise.