Bolt on items like you have now and a bolt on Supercharger with stock tune, should not void your warranty depending on what items are being warrantied. Pulling the heads off and camming it up, I would imagine that it WILL instantaneously void your warranty for the motor related items anyway.
In the end, the factory warranty or factory extended warranty is to just cover defects, NOT to cover items that wear out due to normal wear and tear. That is why worn out brakes, tires, windshield wipers, etc. are all NOT covered, even on a full ****-Care warranty. They are a part of normal wear and tear.
Extended warranties should only be looked at for replacing faulty items. An A/C unit goes, that is warranty. Your heater core leaks, that is warranty, your radio dies, that is warranty. You hop up the motor and the clutch goes, I would not hold my breath that I would get any warranty taken care of on it. You added a bunch of horsepower and pre-maturely wore out a wearable item to start with. However if you add all that power and an ABS rim sensor dies, that is warrantied. A gauge is pretty much warrantied in all instances as who touches them?
If you are going make major mods, then you are accepting the risk of breakage and why should they warranty it after those changes? You took ownership at that point and it is your responsibility.
However if you take great care of your vehicle and you are not racing it every weekend, you do not peel out of the dealership hell bent for leather, than why would the service manager not at least understand your benefit of the doubt? Treat the service manager and service technicians with respect. Never get argumentative. Always bring your vehicle in clean and polished so they can see you have pride and respect in your vehicles. Just present the problem and be profession and let them do their job. If you come in demanding that they fix everything and that it is them that is causing this major inconvenience for you, then I doubt you will get anywhere.
The only problems I have ever had with vehicle warranty service on any of my vehicles stock and modified, was on a brand new 07' Jeep SRT8. They basically would not fix anything period that was wrong with the vehicle and I bought a factory Maxicare Warranty, but that was a dealership thing . I worked with Jeep to get the service transferred to a different dealership and never had another problem with it after that. It was 100% stock too and I had bought it from that dealership, so I guess it happens.
Anyway, just like any confrontation, be professional, calm cool and collected and you will have the best chance at success. Come in like some punk demanding the world and ordering people around and you will not get anywhere, not even on a 100% stock vehicle. IMHO
In the end, just use common sense and look at the whole situation. If you add a bunch of power and then bind up the rear diff, should you get warranty? I mean should you really?