Well... It is pretty much doing the same thing as the Autoleveler program is doing. Only it is compensating for the table error at the output (motors), not the input (G code).
The map file can be created manually. But what a pain in the rear! So Brett wrote a Wizard that generates a G code probing routine to automate the mapping. Of course this requires the use of a touch probe though. You can specify the resolution required and the area of the table you wish to map. For the base table map, one would obviously do the whole table area. As for the resolution, you need to make is fine enough for your application. The error map is interpolated between the map points. This is what I would call the base table map.
After you have the base table map (or your table is flat and you don't need base table map compensation), you can just load a map for a particular part. This is almost exactly as you describe with the Autoleveler process with the exception that the G code is not modified and instead, the produced map file is loaded.
For warped/bowed PCBs, one would necessarily have to "map" the board each time a new board is done. But for getting rid of table error, the base table map only needs to be done once. So this will work perfect for the OP's issue.
This table mapping isn't using the override axes. However, the THC control does indeed use that. THC control will also be front and center in the next release.
Steve