As I understand it, 'smart' batteries cannot measure the charge currently contained within themselves (there is something awful about that sentence, but I think its OK).

The charge is measured as it enters and leaves the battery. When you recalibrate a battery by charging it full, discharging fully, then charging fully again this resets the 'charge-o-meter' to 100%.
Thats how Apple laptop batteries work at any rate. If yours is as smart, it should be able to recalibrate itself to a new battery. I confess I don't know much about the variations of currents and voltages used to recharge batteries and their associated tolerances. I would guess that a nasty miscalculation of this is the sort of thing that could make a battery explode.
3rd party batteries with higher capacities seem to work fine with Apple PMUs, SMCs etc. As far as I know, the electronics are identical to Apple batteries but the actual cells are upgraded.