A control system operable to train a control tuner to generate temperature setpoint tracking improvements for a thermal processing system is provided. In one example implementation, temperature setpoint tracking improvements are achieved by generating system controller parameter adjustments based on a difference between a simulated workpiece temperature estimate and an actual workpiece temperature estimate. For example, a system model can generate a simulated workpiece temperature estimate simulating an actual workpiece temperature estimate, and based on the difference between the simulated and actual workpiece temperature estimates, generate clone controller parameter adjustments. The clone controller parameter adjustments can be used to generate system controller parameter adjustments, which can improve temperature setpoint tracking for the thermal processing system.