The thing is this:
When you do a fully-fledged launch in any car, there will obviously be a lot of stress in the components, as high forces are involved. Usually, one of the components gives in in some way. May it be the engine by dropping its revs, the tires by spinning or the clutch by slipping, you seldomly combine all these factors in perfect harmony to create the perfect launch. If you do however, it is logical that all the forces go into the drivetrain, as there is no other part to "vent".
Now, with the GT-R, we have a high-grip AWD system which prevents the wheels from spinning too much and thus eating up the enourmous forces of the 480 bhp engine (obviously, the overall power of the car also plays a role here). Then, there's a launch control (LC) which makes sure that none of the power is lost at the clutch or too-low revs. So in the end, what you do with a GT-R-LC-start is load the absolute maximum of forces you can archieve onto the drivetrain. No wonder that if you do that repeatedly, there will be a part that will finally give in.
That's why Nissan says you shouldn't do this. I'm pretty sure they'll be alright when you have some kind of warranted damage on the car, and they discover that you've done it once or twice. But there's a limit for everything, and if you exceed that limit, your warranty is void. Every manufcturer includes similar things in their handbook, and as the GT-R's manual states that you shouldn't turn VDC off at all and says nothing about the LC, it is obvious that their misuse will void the warranty.