The control loop will adjust the duty-cycle for you and maintain the output voltage constant, so the output voltage will be set not by the input voltage but by the divider and reference. The duty-cycle will change according to the INSTANTANEOUS input voltage, keeping the output constant.
To get an idea of where the average duty-cycle will be, just use the average input voltage. The maximum duty-cycle will correspond to the minimum instantaneous voltage and the minimum duty-cycle will occur for the maximum instantaneous input.
But to calculate the transistor current always use the minimum instantaneous voltage, for a worst-case scenario.