Well basically the B6 and the B7 are the same car, just an evolution. Styling wise I personally think for the worse.
You shouldnt need to worry about the can gateway and you may find the canbus electronics are more co-operative.
Yes you might need to add the gps antenna, depends on whether the cars own one can be interfaced simply by the right fakra to rp-sma adapter, and the same goes for mic. but its really not a big deal to add them if youre capable with car wiring.
Over time the B6 and then the B7 evolved in steps for both specification of equipment and electronics, what model and year is better put to those more familiar, the last Passat I had was a 56 plate SEL.
As for the diversity antenna, youll lose that, a lot of the antenna adapters for the installation just parallel the antennas, this is not a good thing and why many find they cannot get decent radio reception later. Instead you pick the primary antenna and use a booster to that. You also need to know if the B7 FM antennas are independently amplified or whether that function was via the oem head unit, because if theyre not independently amplified you need a booster adapter instead, because aftermarket units do not amplify the antenna.
Also, if the car had DAB and the unit you you would also need to investigate if the right fakra adapter exists for that too.
Its not exactly complicated, but neither is it simple, which is where a lot of people go wrong making simplistic assumptions.
There are plenty here who can elaborate further, often with the right knowledge and adapters a lot of the cars original items can be repurposed if you do it properly.