You are making a major modification to the vehicle, putting it under more stress than the original design. The manufacturer can, and most likely will, void the entire vehicle powertrain warranty. Because of the increased power and torque, I could see this even extending to the body structure, suspension, glass seal leakage, etc. If aware of changes to the vehicle electronics, I could see them denying a claim for sensors, electronic control modules, emissions, etc.
The fact of the matter is, if you are going to make such a major modification, you should expect at least a full powertrain warranty void/flag by the manufacturer (any manufacturer). If this is something that one can not accept the risk (payout to fix broken parts), then it should be left alone.
The vehicle manufacturer extended the warranty based on the factory configuration of the vehicle where the design and testing has shown that the vehicle is not expected to experience significant failure of components. There is no rational argument to expect that they should provide warranty coverage for components that fail from non factory modifications.
The best thing to do, is to get friendly with your local service manger and discuss with him/her to get an understanding of what his/her reaction would be to a warranty claim for something unrelated. For example, there should not be an issue if you had a claim for a failed seat heater, gauge, etc.. However, it is wrong to expect something to be repaired that has failed when associated with the modification.
A warranty is basically a contract between the manufacturer and the owner. They will provide coverage for failures as long as the vehicle is maintained as manufactured, and all of the required maintenance work is performed (and records kept). It goes no further than that.
Fraudulent warranty claims over the years has made life more difficult for everyone, and the manufacturers may sometimes overstep the bounds of reason. When faced with millions in potential fraudulent claims, they had to do something.
As mentioned, getting to know the service manger first is a big part of the issue. When I had my SRT-4, me and my service manger had a clear understanding, he knew exactly what I was going to do to the car, but he also knew I was not going to try and pass off a claim for something I broke.
The stock clutch was toast shortly after the MoPar stage 2 upgrade went in, and I had a ceramic composite Spec 2 clutch installed by the dealer. There was an issue with it not wanting to disengage. Discussion with STAR technicians hinted at a possible issue with the hydraulic actuator for the clutch. They wanted to know upfront WHY the clutch was being replaced, and the SM told them I was having it done, it was not a warranty claim. They were fine after that assurance by the SM. Turned out it was a defect in the clutch disc (high spot) and Spec replaced it.
Even the regional rep had walked though several times and saw mine sitting there with M&H slicks on the front. I never had an issue with a legitimate warranty claim, and they never flagged my vehicle either.