Didn't really read the article in depth, but i assume they are building all the r&d into it and gorilla mathing their way to a per car cost. In reality though, no GM isn't losing $40k a car. The r&d is already spent. Some capitalized, some cash costs.
Japan's govt subsidized the prius IIRC and Toyota didn't start making money on the Prius until a couple years ago. The Volt is a longterm bet by GM and is the type of forward thinking that a business has to engage in to stay healthy over longer cycles.