As Silver noted, it really depends on the dealer you work with. In reality, if you lower and a bushing goes or something in the suspension, a dealer could state that the lowering caused the issue and thus no warranty coverage. Similarly for the muffler (ie: your cat goes - blame it on you changing the muffler).
For me, I have bought 3 cars from the same dealer and salesman and I do all warranty work through them. They treat me nice and never made an issue of aftermarket add-ons with my previous cars.