I think we all knew this more or less, but it is very helpful to know exactly what kind of instructions the dealers are getting. If I had to do it all over again, I would definitely buy my vehicle from a known mod-friendly dealer.
I'm totally OK with taking responsibility for any failure caused by my own modifications - I think it is dishonest to break your car and try to cover up the true cause if your mods really did cause the problem. I think what most of us have a problem with is dealers using mods as a loophole when any reasonable person could clearly see that your mods did not cause the failure in question. I don't expect a mod-friendly dealership to do anything inappropriate, but I would expect them to work with me on a reasonable assessment of whether or not the failure was due to my mods or not.
We all know there are known issues with various parts of the engine, drivetrain, etc. When you have a dealership trying to blame your mods for a well-known problem that affects a broad set of cars, some stock, some modded - that's when you need a mod-friendly dealer to step in and back you up. Unfortunately, my dealership is about as clueless as they come. I took my V in for the notorious wheel click problem and they were like "what the heck is THAT?". I knew right then that I was going to have to explain in painful detail every single problem I came across. And if I had a major failure and had modified the car, there's no way they'd back anything up because they just don't have enough knowledge or confidence to do so.