I've done some research and I think I can answer my own question. Preamp circuits vary a lot but typically have several gain stages. The gain knob on a real amp controls a signal amplitude adjustment that is typically not placed before the first gain stage. For example, Fenders & Marshalls typically have the input gain located between the first and second gain stages. On some amps the gain knob adjusts signal amplitude at several points in the preamp circuit. This explains why boosting a signal into the front of an amp gives a different result to turning the gain knob, and also why the Kemper can't know how the amp would react at different gain settings by sending a range of signal amplitudes into the amp input.
So I can see why a Kemper profile would struggle to react accurately to a change in the gain setting from the original as-profiled gain setting. For a non-liquid profile, changing the gain setting is ( I think) simply adjusting the input signal before the first gain stage, which would not be accurate to the amp.