The new TDI uses a conventional air to air intercooler for charge cooling. It uses coolant to cool the fuel though. There is a seperate small coolant circuit that runs through an isolated tube in the top of the rad and cools a small amount of coolant to near ambient temp. This coolant is then used in a coolant/fuel exchanger to cool the return fuel. The PD engine runs the fuel through the head quite close to the combustion chamber and puts a fair bit of heat into it, making the fuel cooler necessary.
I seriously considered a air/water IC when I built my IC setup. The only problem that I noted with water cooled intercoolers is the dual heat exchange. The coolant/air rad cannot quite cool the cooling medium to ambient and the air/coolant rad that cools the charge cannot cool it to the temp of the coolant. Efficiency takes a double hit. Water cooled intercoolers are used to good advantage with an ice box for drag racing. They are also often used to solve serious packaging problems (blown mustangs come to mind) that simply cannot use an air/air IC. They also have an advantage in continuous high load conditions as they take longer to "soak".
Looks like there are a few different OEM units. Thanks for the info guys...
PS - reason I asked: The A1 NA Diesel intake manifold has a big rectangular opening that for a turbo-diesel application might be "cool" (literally

) to weld an air-water core directly to:

It would make for a pretty tidy intercooler install, with the boost tubes not being much longer than they would be unintercooled.