Most dealers which do a healthy trade in AM parts will be more inclined to be fair on warranty work. There's enough of them around to be sure that wherever you go, there's a good chance some local dealer will look at your tranny issue (for example) and understand that a CAI didn't cause the problem. The truth is, look at what you're changing, try to understand what is has the potential to break, then work out your risk is from there.
I've been to a number of dealers with my car and had a bunch of warranty work done without any trouble. There's a lot of myth in here on this, and also some good threads from guys who actually know what they're talking about. Try searching and tracking down some of those threads - some are EXTREMELY helpful. I'm new to modding too, so only speak from my experience.
For things like "flashing the computer", I don't even know what that means - writing and designing software applications is what I do for a living, and it strikes me that the handheld tuners out there should only adjust parameters in the computer, not re-write the system, so how this would "void" a warranty, I dunno. I mean, if you buy new wheels/tires and they have a different tread circumference, you need to adjust the cpu to account for this. I recently saw a thread where a tech stated that the dealer CANNOT tell if you've "flashed" your computer. This would bear out the idea that a "flash" is merely a parameter tweak.
Ultimately, the risk is yours. I've heard horror stories where dealers have been @sses about mods which could in no way have caused part failures, but have tried to deny warranty work. Since these stories exist, there must be dealers out there who'll try that on, so Alec's cautionary word above is valid - you may end up broken down in the town where the only dealership will not even look at doing warranty work 'cos you've stuck a pair of CDC louvres on!