The 'rotate with the special tool' thing is to lock the variable camshaft advance mechanism back to it's zero point. It is probably supposed to do this on shut down, but when you are retiming the engine, you best be sure things are locked in.
The 'breaking loose of the cam gears' thing is to ensure precise timing, given such a long belt. Without breaking them loose, the accuracy is based only on the number of teeth between things. With 4 variable cams, and a very long timing belt, Audi feels that there is not enough accuracy. As such, they have used a timing method whereby the cam gears are infinitely adjustable. Everything can theoretically be dialed in with a fair amount of precision.
The way that deyrag replaced his belt mimics that of a convential V6 timing belt job (like on say, a Hyundai or Toyota). He used the cam and crank locks to merely hold things still while he swapped the belt out "tooth for tooth". The variance between the 2 belts is never adjusted for. Nothing is dialed in, nothing is changed. It all stays the same. This is generally good enough (and is certainly good enough for Toyota and Hyundai). However, with 4 continuously variable camshafts (and software by Audi), the 3.0 tends to be pretty picky. This 'cheater' t-belt method sometimes works out ok. And sometimes can result in timing that is off just enough to cause a VVT fault code.
The real test is to pull up Measuring blocks 090-093 in VCDS after you're done. This will show you how close you got to 'perfect'. There is a specification in the Bentley manual for what is considered satisfactory.
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