It will actually charge bigger batteries more full than smaller ones, because the end of charge threshold is fixed at 50mA (iirc). Well, PR1.3 introduced a feature/bug where the phone is constantly drawing 80mA, so end of charge threshold is never reached, and it just floats the voltage at 4.2V. In theory this causes extra wear and tear on the battery, but it's hard to say if it makes any difference in practice, other than that the battery stays absolutely full staying on charger very long.