This is the better way of determining random noise levels in test patches. I don't know if DxO uses that to reduce the fixed pattern noise e.g. caused by amplifier variations.
DxO said that their noise figures include fixed pattern noise. Your approach would, as you indicate, not see the fixed pattern noise. Fixed pattern noise should be reported as it can be substantial part of the noise at high ISO (at least in the 5D2 generation cameras - not sure about the K-5 generation).
What I expect
DxO does is generate a smoothed polynomial describing the spatial intensity of the light reflected off the patch.
An then subsract this background level from each pixel to determine noise. This compensates for low-frequency gradients (non-uniformity due to lighting, filters, vignetting) which are not perceived as noise by observers. In fact, humans hardly see such low-frequency gradients at all. And this technique would measure high-frequency (temporal and fixed) variations which are perceived as noise.
The statement by DxO that FPN is included in their noise figures is consistent with their protocol which mentions that it is important that the test targets are cleaned (dusted?) regularly. Dust on the test target would be measured as noise. It is also consistent with their avoidance of printed targets which tend to have some degree of noise.