The majority of cars on the road are indeed obd2 but most new wave models of vags have to have the ecu removed and flashed as previously mentioned.
The facelift 2010 on vw t5 is a particular nightmare due to the position of the ecu which has to be removed, the pre 2010 models are a breeze taking about 30 mins through the obd2 port.
A lot of other brands are going this way for example here is a 2011 nissan navara we did last week-
The older models used obd2 like everything else, we have had to spend an additional £2000 on the jig equipment for these latest models and only the dealers havereplacement tamper bolts.
We advise the customer that the manufactuers warranty will be void, howeverthe tuning company we use for the maps do offer a warranty scheme for vehicles with up to 90,000 miles, and with vag models the new software will be traceable.
I am unsure of the up as we have not had one in yet but i do not see why itwould be any different to the new platforms above it.
If you look at the majority of ecu tuners you will se a vast difference in pricing when comparing new models to older models and this is because it is no longer a simple plug in process.
I have several vehicles here belonging to usthat we have mapped through obd2 and even alittle dragcarwith aftermarket autronic management that is far more complicated than any "chip" tuningbut the 2011 scirroco and 2012 vw T5 i have left alone as i do not relish the thought of explaining to the dealer why there are standard fastners fixing the ecu in place.
If you are after bang for your buck I could supply youa won nitrous kit that would give you an extra 25-150 bhp for £600 and as long as you fitted a new hp fuel line and intake hose before you took it in to vw nobodywould be any wiser !