The knobs have always matched. Multi-point Iterative Matching Technology (MIMT) extracts pertinent data from various points in the amp's circuitry to correct the model. A model can deviate from the actual amp due to parasitics, i.e. coupling between various points in the circuit, through the chassis, etc. as well as non-ideal behavior of transformers and other components. It is impossible to predict the deviations since they are not "designed in" and are not reflected in the schematic. In some cases these "imperfections" are happy accidents and give an amp it's character. Older amps, with their point-to-point wiring, are especially susceptible to this although I'm seeing it in some modern amps too.
The advantage to this multi-point approach is that we correct the model at various points in the circuit rather than just doing a match on the output.
This has the effect of making the models extremely accurate across all possible settings of the various controls (I'm actually laughing here at times that the controls track so well). The difference tends to be subtle in many cases but it is audible and, after all, we are striving for perfection. Another advantage is that it cleans up mistakes in the model so if a value was entered incorrectly, MIMT will correct the mistake automatically. Furthermore, the matching data makes it easier to find mistakes since I plot the data prior to saving and embedding and if the data indicates significant deviation then I know something is incorrect. For example, I have found at least 10 mistakes in the last two days. That 65 Bassman model was way off. The MIMT data showed significant deviations so I knew something was wrong. Turns out I had the Tone Stack Frequency multiplier set to 4.0 (should be 1.0) so the tone stack was off by a factor of four.