Yes and no. Yes, when everything is working correctly. No if there is a failure of the electronics or firmware or your configuration files and 100% PWM gets applied by mistake. So if 100% PWM would risk a fire or cause severe economic damage, then you shouldn't rely on restricting the PWM to limit the temperature rise unless you also use a thermal cutout.
What type of heater is it? If it's a DC heater, you could reduce the voltage to reduce the heater power. If it's an AC heater, you may be able to halve the power by connecting a diode in series with it.