The current crop of economists parse all commodities into money - which in the process nullifies all physical differences between the commodities themselves.

Well, presumably the current crop believes that prices are the result of marginal conditions (the intercept of supply and demand), which means that the prices themselves are specific to a particular set of circumstances. This has always been a problem with aggregate measures like GDP, national wealth, and the like. Various policies, reallocations, etc., change the prices, or so the theory goes. Economists frequently ignore their own theory on this point, though...

More to the point, I've been lurking these boards for a little over a month, and a lot of the issues related to energy "aggregation" remind me of the capital controversies that have emerged over various periods in the development of economic thought. The Cambridge rounds seem the most relevant, when the question was roughly about whether capital could be sensibly thought of as some aggregate, in the presence of heterogeneity of the underlying goods (the "sensible" applies to the notion of a supply of capital). A billion dollars of tractors cannot be magically turned into a billion dollars of greenhouses...