Well, as Audi knows what they're doing I think we can safely conclude that is not the case.
Why do you think it would generate more drag? The front profile of the car looks exactly the same to the air. This just means the rear wing bottom surface is as clean as possible. As far as putting the wing as far back as possible, I'm sure there's some sort of 'envelope' it must be positioned within. In any case, putting the wing as far back as possible makes the car more pitch sensitive; or, rather, has a greater effect on the pitch of the car as speed increases and that's a bad thing. In an ideal world you'd have all of the downforce centred over top of the wheels, really, but that's not possible.
Regardless of the all the interplay effects, Audi would not have done it if it were worse than what everyone else was running.
GT3's success is pretty much completely down to it being a pay-driver model. There are pro teams, but the category started as a gentleman's cup and the vast majority of the cars are in the hands of amateur drivers. There is the distinct possibility that this GT2 cup could siphon those drivers out of GT3, reducing the ranks there. Which isn't really a bad thing, necessarily, if GT3 is being reshaped as an all-pro category. But sports car racing has always relied heavily on the presence of privateers and pay drivers, so it very well could be what starts the decline of that category.
