I just sent Rich a note at FoCal asking him if the QoF results can be used as an indication of the "real world" image quality differences between two D800 camera bodies if you test both with all the same settings and shoot the same target with identical lighting and distance to target (side-by-side testing).
So far, my testing of my D800 and D800E show significant differences at all apertures and all lens...the D800E produces higher QoF results. However, I have to zoom images of the targets to above 100% to see any difference in them except contrast. If I do an extreme zoom to say 800%, I can see definite differences in edge transitions from black to white. It takes the D800 about 15-20% more pixel widths to transition from black to white.
If I zoom to 67% which is typical of what you would see in a 24" x 16" print hanging on a wall, I can see no difference in details after I process for contrast differences.
I don't know what zoom level FoCal is actually using for its testing, but it must be well above 100% for it to see the differences in the D800 and D800E test shots.