One thing to watch for is that some lens problems are showing up and incorrectly being attributed to the camera. An incorrectly positioned lens element can result in the same results you reported. If you are going to send in your camera, you might want to send the lens with it.
Focus inconsistency is different than a consistent focus error. On my D800E I get the same error every time with the far left focus point. On the far right I get a small but repeatable focus error. The errors are very consistent - same direction and amount of error. And my center sensor is quite reliable and accurate.
Even the center sensor performing to spec its going to have variation, but it tends to be tightly ranged small misses. And you won't be likely to ever find a lens and camera combination that performs as well with outer sensors as the center sensor. The resolution of the D800 shows errors you could not see on earlier cameras.
I've also seen reports of missed focus with other variables that Richard mentioned. ISO, WB, and distance to the subject all can produce inconsistent results and false errors.
Your focus technique can also make a difference as to whether errors make much difference. If you focus and reframe, tracking can cause focus errors. If you use the shutter to activate focus, you need to position the sensor over a good focus target. Back button focus tends to allow you to increase use of the center sensor which is the most accurate.
With all these potential sources of error and different testing methodologies, it's probably better that we leave it up to each individual to assess their own cameras and course of action. If you feel you are having a significant problem, by all means have it fixed.
As far as the repair, I have heard more reports of proper repairs than of problems. But some of the problems have been pretty bad. I'm going slow on having my D800E repaired since the central group of sensors is pretty good.