Hi kim
You are operating on the assumption that you get 1 LSB in the 41-bit register per Wh of energy. But that is not necessarily true. You can scale the amount of energy that each LSB of the 16-bit register will correspond to. In fact, in practical cases, the weight of each LSB comes out to be very small, thus giving you good resolution to measure energy and to help you make sure that no significant amount of energy goes unaccounted. For example, refer to page 51 of the datasheet (RevE) where a sample calculation is shown; the Wh/LSB comes out to only 0.0002820.
Does this clear your doubt?
Regards
hmani