Tuning and breathing mods definitely won't break your warranty. Some (many?) dealerships are shady, and some would give you a runaround about it, but they'll lose if you stick to your guns, assuming the mod didn't actually cause the problem you're claiming under warranty.
Even if something catastrophic did happen (which was unrelated to your mods), you could reflash the ECU and/or remove a mod or two if you wanted less dealership hassle. Better idea is to develop a good relationship with a good dealership, have them do some of your install work to boot.
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