There are dealerships that install/do after-market (lift-kits, bigger tires,...etc...etc) work and cover it under the warranty...Some I know of:
Adams Jeep of Maryland, Susquehanna Dodge Chrysler Jeep, Stetler Dodge Chrysler Jeep...
Guess you should have asked before making your purchase....Doh
If the work is done correctly I wouldn't worry about it. Just be sure your "gearing" is correct to the lift and tires.