No, as I said, it does NOT know if you are running 3 separate phases or the same phase through all three poles, it SPECIFICALLY INSTRUCTS you to run the circuit in series through the 3 poles for single phase.
But again, WHAT IS THE CURRENT going through to the motor? Just because your motor FLA is 40A, does not mean it is actually drawing that much. The current draw is based on the actual LOAD on the motor. If it is set for 45A (probably incorrect by the way*) but the motor is drawing less than 15A, then it will trip on phase loss because that's what it does.
* the OL setting should be at the motor nameplate FLA. The NEC section stating that you can have an OL relay start protecting at 115% is not the same thing. The relay ALREADY factors the 115% into the trip curve. So if you set it at 115%, you are setting it at 115% of 115% and you can lose the motor.