Turbotax is not working as far as the ACA once again. It is adding the ACA overpayment to the tax you may owe and then using this number to base any penalties owed. In other words there is "no added penalty for taking extra subsidies". The software should ONLY be looking at the tax you would owe "without" adding the ACA over payment to is (and then base a penalty on this number). So if say you owe $500 in taxes and you also owe $2,000 for a ACA overpayment your taxes owed are $2500 which is over $1,000 and Turbotax in now adding a penalty. But in reality turbotax should only look at the $500 you owe (and not the added $2K ACA overpayment) and therefore you do not owe ANY penalty - what out!
