Yeah the profit margin is about $5000 on the ES. Its closer to $10,000 on the LS and the SUVs.
Its not really cost of production that drives the markup, the profit is kept by the dealership not Lexus. Lexus sells them at wholesale which includes the cost of production and their profit. Whatever the dealer can get above wholesale is their profit, plus holdback. The salesman makes a commission on the profit made by the dealership. Most dealerships don't buy their inventory anymore they actually rent it when it sits on the lot, then they pay Lexus wholesale less holdback when the car is sold. How much of the markup they get to keep is a direct function of supply and demand. The longer the car sits on their lot, the more it costs them in rental fees and insurance and that eats into the profit, thats why dealers have to sell the cars quickly. I can not imagine any reason to take a $6,000 hit on a current model year car though, that has to be BS.
When I bought my car the MSRP was $39675 and I got it for $35k even plus tax and title. That was $4,675 off the list price and it was ALMOST invoice. That was an excellent deal and it was unbeatable in the DC Metro area at the time. I've seen nothing to make me think that the market for ES, especially the refreshed 05 is any softer now, I bought my car in January which is the slowest month in the car business.