I have had a couple of KLs with the sunroof but I never opened them but to test them before I bought the vehicle so never had any squeaks. My current TH does not have the sunroof as I preferred to put that money toward the Safety Tech Group and the memory ventilated seats. Everybody has their own preferences and the sunroof probably does help with resale and you may have all the options, but to me I like metal over my head just in case something should happen where it is on the ground--hope it never happens. But to answer your question, the dealer should be able to correct the noise coming from the sunroof or you might go to another dealer and see if that dealer can be more of a help about your concern.
2017 Trailhawk L Plus 4 bX4,Rhino exterior,Power 8 way drivers seat, Willys in windshidel,Cold Weather Group, Comfort/Convenience Group,Trailer Tow Group, 3.2 -Liter V6, Black Hood Decal , Uconnect 8.4 , Safety Tech Group, Leather Interior Group, Ventilated/Memory seat Group,Navigation. No hole in roof.