Genuine VAG-COM cables have security/dongle built in which stops you having to register the software to get more functionality. You can't change anything in the ECU with a VAG_COM cable.
ODB2 is an international standard which outputs info from the ECU. VAG-COM is just a nice way of looking at the information and tells you a lot more than the raw data.
I think an ebay cable and 409 would be a cheap and not overly complicated purchase to use on a MK3. If you want to look at MK4s then a proper cable with CAN-BUS is the way to go.
I have a flash cable and there are plenty of ECUs that can't communicate with, even in MK4s.
Gavin
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