With the D3200 I believe it says in the manual that CDAF is generally inferior to PDAF. I expect is says the same in the D800 manual.
I think you are right, the fine tuning only applies to PDAF, not CDAF. It makes sense... CDAF is looking at actual data from the sensor and trying to optimize it by getting sharp edges between pixels. Throwing in a fudge factor should only make it worse from there.
I think you owe it to yourself to try manual focus in live view. First use CDAF, then mess up the focus, and then do in manually, zoomed all the way in. There are people who use a magnifying glass to look at the LCD.
