You need VAG-COM for several things:
1) to change the coding of your instruments so the navigation instructions appear on the DIS. Also, on some models, to code the CAN gateway.
2) to check, and correct, the coding of the RNS-E so it is correct for YOUR car.
3) to clear the fault codes that are bound to appear on the RNS-E while you are installing it - usually things like bad antenna connection (because you haven't connected it yet!), intermittent communication (because you plugged it in and out a few times), etc.
Sometimes you can get away without needing a VAG-COM, but not usually.
A correctly setup VAG-COM leaves no trace for the dealer to be able to see what you've been doing!