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A scientific reason people speak of being "carbon" neutral rather than CO2 neutral is because CO2 is the result of efficiently burning anything with carbon in it (gasoline, diesel, biodiesel, ethanol, etc.) On the simplest level, tracking carbon useage for energy production is synonymous with tracking CO2 - it's just whether you focus on the reactants or the products. In general it makes more sense to focus on the reactants that way you delineate the fuel from the utilization technology (IC engine, turbine, fuel cell).
If you choose to discuss CO2 only, you cannot do a life-cycle cost very easily. Fuels with carbon produce CO2 on burning, trees and other plants convert CO2 to carbohydrates, oceans absorb CO2 and convert it to carbonic acid (H2CO3). Because carbon is the common element, no pun intended, in all of these compounds, it is simplest to track the fate of carbon atoms rather than CO2 molecules. Basically, instead of listing all of the reactions which produce or consume CO2, you track the common element, carbon.
