Disappointing to read about your story, Wallace.
As it turns out - you didn't even buy the Mesa Red after all, which leaves me baffled as to why you were only offered the white. Yes - Lexus Stoke may have a white one they want to get rid of due to age or other factors, but if money can't help the colour i'm baffled as to why they didn't at least explore other options than simply white if a Mesa Red won't arrive till September. Their loss it appears!
Trade in price should never be massively different between dealers, as they all work from the same guides. However, one thing I would say is it always amazed me (back in the days when I sold cars) how people were almost insulted that a scuff, alloy curb or dent etc would affect the value of their car. For example - the Lexus Approved Used programme dictates that all cars should be prepared to a high standard. A customer simply won't accept a car with 4 curbed wheels, a dent or scuff or any other major marks beyond "fair wear & tear"... if there are marks on used cars, the dealers are the first ones to be told "I won't buy that unless its paited / repaired", so why should a dealer ignore damage to a car when valuing it?
From my point of view, it is simple logic. A curbed wheel refurbished to Lexus standards is not cheap. Neither is other bodywork generally - so if I were to visit a dealer with a car that required some work to bring it up to Dealer standards (which, lets face it, nearly all cars do), I'd find it pretty normal that they take off an amount to allow for the refurbishment.
In the end - you got a car you are happy with and service to match, which is all that matters. The IS300h is a fantastic car, i'm certain you'll enjoy it.