Having only driven the FSI a couple of times, I am not sufficiently familiar with the rattle (although I certainly remember it) to diagnose what is causing it.
Audi say that it is indicative of the engine and that it it is not a fault, merely a characteristic of FSI technology. As the earliest engines are now approaching 6-8 years of age there does not seem to be a reliability issue with them, so we can only presume that Audi are right in this case and that the rattles are nothing to worry about, as long as they soon disappear after the engine is warm.
Cheers,
Mike