I don't know about the legal ramifications of your agreement, but I do know that you do NOT want them to "install" a sunroof on your new truck! I don't think they could do that without tearing up the roof, and you don't want to take the chance of having leaks or whatever.
On mine, the side view mirror was messed up, so they decided to switch out the entire driver's side door ... they seemed to act like it was an easy enough thing to do, but I can't imagine there being a simple way to "install" a sunroof on your 4Runner if it doesn't already have one ... and I certainly would not recommend it!