My D800E AF consistency tests showed more erratic behavior than the D800 which lead me to believe the greater detail/contrast/sharpness the D800E captures, as shown by the tests results, caused the difference. Perhaps FoCal is more sensitive to sharpness/contrast/details than it should be...resulting in inconsistent results.
However, when I ran AF Fine Tuning with the same lens on the D800E on different days, I ended up with the FT adjustment either the same or within one point. FoCal must have factored in the inconsistency in its curve fitting to come up with basically the same adjustment.
Keep in mind that the software was originally developed with Canon camera bodies and before the 5DMIII and D4/D800 came out. I think the developer is still playing catch up with the newer cameras with larger pixel counts. Just a guess.