First, you need to be aware of the differences between factory warranty and ESP. No matter what folks like to call it, the Extended Service Plan is NOT an extension of the factory warranty, it's a service contract and as such it comes with it's own set of rules which are spelled out in the contract. Any questions concerning coverage should be addressed to the administrator of the ESP, and I wouldn't just take the word of the guy trying to sell you the plan since we all know how accurate those discussions tend to be.
Obviously, nonstandard parts will not be covered under the factory warranty. Further, if your nonstandard parts cause a failure to other parts, those will also not be covered. Federal warranty law requires the warrantor to prove that your modification was the proximate cause of the failure, however, before they can legally deny coverage. When you start talking about the ESP, however, the federal law does not apply.
In practice, most folks don't have a problem if the mods are limited to the basics like lower restriction intake and exhaust plus a tune. When talking about major infusions of power, with headwork, cams, added displacement, etc., then you might find yourself fighting a losing battle. Yes, some dealers will look the other way and still submit the claims as if the bike were stock. But that isn't a given, and if your dealer won't do so you would have no legal basis to fight him.
Caveat emptor.
Jerry