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let me see if I can re-phrase my question.
1. OK, heat engines are not 100% efficient because entropy change in the
hot reservoir must be compensated for by entropy change in the cold
reservoir;
2. Batteries (fuel cells, etc.) additionally have entropy changes
related to chemical potential. So (I'm a little fuzzy on the exact
calculation but) again tracking the entropy of the chemicals before and
after they react in the battery we can say that we won't get all of the
energy out in a useful form because entropy has to increase (or remain
constant at best).