1. A temperature control system for a thermal reactor having a process chamber, the control system comprising: a first control loop comprising a conventional controller and using a spike temperature sensor signal as input for the conventional controller, which provides an output signal that controls power to a heating element of a thermal reactor, the spike temperature sensor located in proximity to the heating element and spaced from the process chamber; and a second control loop comprising a Model-Based Predictive Controller, using a paddle temperature sensor signal as input for the MBPC, which provides as an output a spike temperature control setpoint that is used as input for the conventional controller in the first control loop, the paddle temperature sensor spaced from the heating element and located inside or in proximity to the process chamber.