Thinking more about this fluttering noise on the overrun, the wastegate is actuated by overpressure in the exhaust manifold, and there shouldn't be overpressure on the overrun. Although the ECU could be opening the wastegate to slow the turbo down.
What happens when you lift your foot off on a TDI engine is that fuel is cut off from the injectors, and the engine becomes an air pump. This will reduce the pressure in the exhaust manifold as there are no hot combustion products. So, maybe with the silencers and catalyst removed, the noise that can be heard is the difference between an engine producing power, with fuel going bang in the cylinders, and an engine in engine-braking mode, with no bangs in the cylinders, just flutter as the air is pushed out of the exhuast valves. Mind you, that still has to make it through the exhaust turbine, which is going to damp it down.