They can only refuse service is the modification causes the problem.
If the cars lowered and something goes wrong with the suspension your screwed. If something goes wrong with the engine your fine. Unless of course it was bottomed out.
I knew before I installed an intake and exhaust on my other car that it couldn't void anything but I called their warranty dept just to make sure I had proof from someone there. It would still be under warranty as long as I didn't hydrolock the engine.