Hi mate,
I've experienced a similar issue with my Golf GT Sport my08 (albeit mine has only done 96,000km). It seems that the noise my engine is generating is more limited to using the air conditioning as it only ever starts once the A/C has been running for roughly 5 mins or longer. If I don't use the A/C at all it never starts. The noise is similar to what you're describing, like a slight clunking noise.
I took the car to a registered VW mechanic when it first started happening and he said that without fully taking the engine bay apart he could not diagnose what was causing it. It takes them at least 6 hours to get into the engine and diagnose anything so I wasn't keen to get it done at the time. He did give me the 99.9% all clear though that it was more than fine to drive but potentially something that should be looked at when I have the spare cash.
Two things I have found through troubleshooting;
1. The noise is only there when sitting idle and not in gear and only after having had the A/C on for more than 5 mins.
2. If the noise is happening and I push in the clutch the noise will stop. Starts again as soon as the clutch is released.
Other than that it seems fairly sporadic. It's been 6 months now and the car has had no dramas but the noise continues to happen in line with the A/C usage. I'm not sure if this helps you at all but thought I would share just in case.
Cheers.
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