As I understood you are comapre real FPGA meaurements with PT netlist measurements. Am I right?
If you measure power consumption on the real FPGA - the measurements are vary (even with the same input vectors) - it's expected. The temperature are vary, the timing slightly vary, the voltage drop, etc ...
When you measure power in PT- the temperature is stable, the timing is stable - nothing vary. The PT produce repeatable results, until you did not change any of inputs : vectors, corners, voltage, etc...
So, if you want to compare, you should compare results of FPGA netlist in PT with ASIC netslist in PT OR real FPGA measurements with real ASIC measurements.