I use the autolevel feature with my 3D printer and it works really well.
But there was several issues within the code that have been cleaned out recently in the dev version. This version will go soon in code freeze so a new release will happrn soon and bring all those improvments.
Btw in the latest dev version they added M codes to control a spindle so it may become even better fit for a CNC.
Now in regards to the the Z probe matrix.
It depends on the firmware and software.
With stock marlin G29 code the autolevel code produces a matrix that later the firmware itself applies at runtime to compensate the height.
For example with GBRL and bCNC it just outputs the height in several points so that the software creates the matrix and later applies the compensation to the commands it sends automatically.
You can even save the matrix values to reuse.
Some others like the ones you mentioned work simillar to this but the process to add the compensation is done manually, so you have some extra steps to create lhe resulting interpolation.
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