with the setup you got, so many factors play in.
I would just take a few normal use caseses and measure temperature, and heater on/off times,
and then perform a "normal" corelation between pwm on/off value and the normally resulting temperature,
and then use that in your product, since supply voltage is constant and known, and resistance is know and not changed a lot,
all you need is the on/off time..
if there is another sensor that could at least tell the ambient temperature to the software,
you can use that value to adjust a bit with.