I'd bet your injectors are stuffed. Ours were replaced at 70,000 km under warranty (thank god) because the car wouldn't idle, ran rough, stalled and sounded similar to yours. The car is now at 115,000 km with no further issues since the injector replacement.
Here's the video I made before the injector replacement: VW Volkswagen Polo 6R TDI 2011 Strange Engine Noise Broken Injectors - YouTube
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