The thinking has always been that oxygen will cause duct closure but the duct will be opened with the prostaglandin infusion and in many conditions the mixed blood will still be deoxygenated despite administration of oxygen.
HLHS and critical aortic stenosis are the only the lesions where pulmonary vasodilation and overcirculation cause real harm but they are very rare and HLHS is likely to have been picked up on an antenatal scan. A good rule of thumb is to aim for preductal saturations >75% before the diagnosis is known.