Yes, the version 2 of the board, is it sensing the die temperature? The board temperature near the FPGA? Does it somehow sense the temperature of the heat sink?
Temperature sensors IC16 to IC19 (see schematics) are placed on the PCB near the FPGA. The measure a mixture between PCB temperature and air temperature below the heat sink. It's not an exact science but this sensors can detect overheating of the heat sink as well as improper installed heat sink (heat sink cold, PCB hot).