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If you take it to the dealer, he will call in the same windshield repair shop you could go to. Sounds like it is going to be an out of pocket expense (not under warranty) so why pay the Lexus dealership their add on percentage of the repair bill.
Is this commonly done on fine scratches? do you recommended bringing in to the dealer?
Garsarno beat me to it--unless the dealer is willing to do so at no cost to you, AND guarantee the work...you are much better off finding a reputable place on your own.
Slightly OT, but--personally, I would never go to a dealer to have them perform third-party aftermarket stuff (i.e., window tint, clear bra, etc.) since odds are they'll source the work out to a third-party shop of their own choosing.