In this case automatic is standard and the manual will be optional. It is possible that it could be the same or more. The last manual shift Lexus was the SC300 in '97. Before that it was the '93 ES300. Since they are developing the new 5 speed just for the US market and will only sell a few, they may charge more. The previous models were slightly less though. Good question.
The manual sounds more like a no charge option since the automatic is standard. My reason is based on the fact that the 17" wheel is standard but the 16" wheel is a no charge option. Besides, options are usually items that will increase the price, not lower it. Unless Lexus starts out the base model with a manual as standard and make the auto an option next year, I don't see the price dropping. But, anything is possible.