Yes, but a fixed ISO rating from DxO should be saying, for a constant N of photons, the 5D3 generates N electrons, and the 6D generates N electrons, at full well capacity. By measuring the ISO at saturation, I believe this negates any influences by sensor filters. With the sensor filter removed, this should lower the ISO rating, for the same quantum efficiency.
Since we know that even the base gains have some (ISO) headroom between the default gain, and actual well saturation (and seems to vary with camera), this should probably be taken into account. And should drive the accuracy of the quantum efficiency results higher, since it's less affected by downstream influences.
If you're looking at sensor efficiency, rather then camera efficiency, I guess.