This isn't so much as a fact, but more along the lines of luck I suppose.
Having a good relationship with your dealership and being honest doesn't hurt.
On the other side of things, yes a tune will void a warranty, on most levels. However, the dealership must prove the modified part in question caused the failure in question.
For example: if person A was to install downpipes and the fuel system failed, the exhaust is in no direct reason responsible for it.
There are a lot of fine lines that come into play when regarding a warranty. The above example would only void the warranty of the parts affected. A tune on the other hand, is much more complex as a tune makes changes to many things and will in turn affect them.
I lucked out in this scenario. I've had a great relationship with my dealership for over a decade and have made probably 90% of my business with them. I was told by the service manager that if I had their lead tech install my parts, they would honor my warranty as long as I didn't "put a rod through the block" or use a different fuel source... (methanol/n2o/etc)