I agree it's not a particularly intuitive bit of software but once you understand it, I dunno... Not an issue for me. If you don't want to use the Sigma dock, you don't have to; Nikon bodies in the 7xxx range and better have an AF Fine Tuning function you can use instead, or you can have Sigma do the calibration for you, or you can forgo calibrating altogether. Being able to calibrate my 35mm at thee different distances is what really made the lens come to life though. It was really, really good before calibration but it's flat out amazing now that it's calibrated. On top of that Sigma calibrated my 50mm lens for free, again at three different distances. And calibrating at all thee distances made a huge difference on that lens as well. My Tamron lens can be focus-calibrated (with a dock) at four different distances AND at three focal different focal-lengths, for a total of twelve calibration points. Both the Tamron and Sigma lenses write the adjustment to the lens firmware, which is nice. The docks also allow me to update the firmware and/or modify certain aspects of my lenses, such as the vibration control.
With my Nikon lenses I have one AF calibration point and that usually means an average, which sucks IMO. Then that information is stored on the camera body and not on the lens, which also sucks, IMO.
Personally... I think these "docks" are one of the best things to come along in a long time and probably accounts for why there is precious little Nikon glass in my bag any more.