Depends, if you buy a vehicle from a yard already modified, it's covered.
My Forester came with pod filter, exhaust, bov. I heard stories about warranty companies not covering because of it, so I wasnt gona bother wit hwarranty, but got it just incase.. sure enough, blew 2nd gear (all the teeth gone, smooth) and they covered it. Also a new clutch not long after, and then a new turbo just before I sold it.
Buying a car from a yard is considered by most warranty companies as a standard vehicle... Much like buying a brand new car, aslong as you don't change what it came with, or use the modifcations to shorten the engines life. I.e running a shit load of boost etc.