The Dock really complicates things. So first you should learn to do the AF adjustment without the Sigma Dock. When you understand that process completely, then if you want you can experiment with the dock.
I would advise to keep the camera setting in place even when using the dock. And use the dock to make offset adjustments for the zoom and distance settings. The camera settings should be at the full focal length of the lens (telephoto) and the normal lensAlign 25xFL test distance (8.2 feet per 100mm).
Then set up the camera and lens for each zoom and distance setting, adjusting the position of the LensAlign properly for each test, and do a test series with the camera still at the original adjustment. If the results are off, then you have to carefully remove the dock (so as not to move the camera), connect it via USB, make a trial adjustment, and then test again. These tests can be done using the AFC-5 setting of FocusTune (AutoFocus Consistency) take at least 10 shots, and then run them through Focustune. After each dock adjustment, test again and readjust the dock until you are happy with the results for that zoom and distance setting.
As you can see this will require dozens of test sequences, and will take a lot of time and require you to be very careful and patient. The dock gives you a lot of flexibility, but will take a huge amount of time and effort on your part.
Hope this provides a rough guide as to how to use the Sigma Dock. It is a comprehensive device, but I do not believe there is a practical way to make all of the adjustments provides. Perhaps just choose a few and then fill in the blank settings by interpolation of other results.
If you have suggestions for improving this process, please send your suggestion in a support ticket. Thanks.