My understanding is that conventional commercial panels are around 12-15%. How is this modelled in HOMER?
HOMER denominates the size of the PV array in terms of kW of rated capacity, not in m². The rated capacity of a PV module, which is the amount of power it produces under standard test conditions, accounts for the panel efficiency. Two modules with the same area and different efficiencies would be of different size. So by dealing with rated capacity, HOMER does not need to know the efficiency.
By the way, HOMER assumes that the output of the PV array is linearly proportional to the incident radiation. Under the standard test conditions at which PV modules are rated, the incident radiation is 1 kW/m². HOMER assumes that if the incident radiation is 0.75 kW/m², a module will produce 75% of its rated output in kW.