Sounds like either your dual mass flywheel is worn (they make a rattling noise once worn) and/or your throw out bearing is worn (although the bearing usually makes more of a whurring noise rather than a rattle).
I had a MK6 GTI that needed the rear main seal replaced and the engine had done around 80,000kms at that stage. To replace the rear main seal the gearbox and clutch needs to be removed - the mechanic said my dual mass flywheel did have some signs of wear but was still ok.
Not sure what causes the dual mass flywheel to wear - whether its simply time/distance travelled or whether how the car is driven (eg driven hard / stop start traffic etc) causes it to wear at different rates on different cars. For reference, my car was a Newcastle city driven car all its life, so no crazy traffic jams or anything.
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