I think I see what your saying, I could see pumping losses while packing the cyliders full of air and fuel for either a turbo or a supercharger, The way that I look at how a turbo works is one of those spinning angel candle x mas things The rising heat from the candles spins the fan thingy ( thingy is the technical term ) there is no wind or blowing air the heat does the work. I hope that makes sence? And I wish I new what that thingy is called but I dont. If exhaust was cold it wouldn't work the same and it would take an equal amount of exhaust pressure to make intake pressure ( that would be your pepetual motion problem ) I hope this answears your question??? Without the wasted free engine heat turbos would not work.
