Not an expert, but I did read the article. The point of the "Case-Shiller" metric is that it is computed on the basis of the same exact property changing hands in different time periods. That way it controls for trends in the product pool.

Or as the article put it: Case-Shiller requires two transactions for the same house,” Lazzara said... It controls for the variability in the quality and size of the homes sold from year to year by measuring the change between houses that sold in one period with the prices of the same houses when they last changed owners. “The repeat sales mechanism is a way of adjusting for the mix of product so that you really are getting an apples-to-apples comparison,” Lazzara said.